init
__all__ = ['AmberCLIBase', 'AmberInputsBase', 'AmberSchemaBase', 'Amber18Inputs', 'Amber18Schema', 'Amber18CLI', 'Amber18Forcefield', 'Amber20Inputs', 'Amber20Schema', 'Amber20CLI', 'Amber20Forcefield', 'Amber22Inputs', 'Amber22Schema', 'Amber22CLI', 'Amber22Forcefield']
¶
Amber18CLI
¶
Bases: AmberCLIBase
Amber18Forcefield
¶
Amber18Inputs
¶
Bases: AmberInputsBase
Amber18Schema
¶
Amber20CLI
¶
Bases: AmberCLIBase
Amber20Forcefield
¶
Amber20Inputs
¶
Bases: AmberInputsBase
Amber20Schema
¶
Amber22CLI
¶
Bases: AmberCLIBase
Amber22Forcefield
¶
Amber22Inputs
¶
Bases: AmberInputsBase
Amber22Schema
¶
AmberCLIBase
¶
Bases: BaseModel, YamlIO, Render
cein = None
¶
Sander option: -cein
input redox state definitions
ceout = None
¶
Sander option: -ceout
output redox state data saved over trajectory
cerestrt = None
¶
Sander option: -cerestrt
redox state definitions, final redox states for restart (same format as cein)
compute_platform = 'pmemd'
¶
cpin = None
¶
Sander option: -cpin
input protonation state definitions
cpout = None
¶
Sander option: -cpout
output protonation state data saved over trajectory
cprestrt = None
¶
Sander option: -cprestart
protonation state definitions, final protonation states for restart (same format as cpin)
evbin = None
¶
Sander option: -evbin
input input for EVB potentials
inpcrd = 'mol.inpcrd'
¶
Sander option: -c
Path to file containing input initial coordinates and (optionally) velocities and periodic box size.
inptraj = None
¶
Sander option: -y
input coordinate sets in trajectory format, when imin=5 or 6
mdcrd = None
¶
Sander option: -x
output coordinate sets saved over trajectory
mden = None
¶
Sander option: -e
output extensive energy data over trajectory (not synchronized with mdcrd or mdvel)
mdfrc = None
¶
Sander option: -frc
output force sets saved over trajectory
mdin = 'md.in'
¶
Sander option: -i
Path to input file for controlling AMBER calculations and operations. Options
specified in [AmberInputsBase][schemas.workflow.amber.inputs.AmberInputsBase] should be in this file.
Below is a non-working example of what this file should look like.
mdinfo = 'md.info'
¶
Sander option: -inf
Path to store the latest
[mdout][schemas.workflow.amber.cli.AmberCLIBase.mdout] and other
simulation progress information. An example is shown below.
NSTEP = 494000 TIME(PS) = 2008.000 TEMP(K) = 301.01 PRESS = 0.0
Etot = -103688.2116 EKtot = 19750.7918 EPtot = -123439.0034
BOND = 691.6081 ANGLE = 1937.7561 DIHED = 1279.1292
UB = 0.0000 IMP = 0.0000 CMAP = 142.8106
1-4 NB = 795.8815 1-4 EEL = 10392.2564 VDWAALS = 18105.7369
EELEC = -156784.1822 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 317340.9390
Density = 1.0364
Ewald error estimate: 0.8100E-04
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps: 500000 | Completed: 494000 ( 98.8%) | Remaining: 6000
|
| Average timings for last 25500 steps:
| Elapsed(s) = 59.89 Per Step(ms) = 2.35
| ns/day = 73.58 seconds/ns = 1174.27
|
| Average timings for all steps:
| Elapsed(s) = 1142.43 Per Step(ms) = 2.31
| ns/day = 74.72 seconds/ns = 1156.31
|
|
| Estimated time remaining: 13.9 seconds.
------------------------------------------------------------------------------
mdout = 'md.out'
¶
Sander option: -o
Output user readable state info and diagnostics. -o stdout will send output to
stdout (i.e., the terminal) instead of to a file. This stream will contain the
following information.
Characteristics of the Amber release.
-------------------------------------------------------
Amber 22 PMEMD 2022
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 22
| Compiled date/time: Thu Apr 14 14:06:37 2022
File paths.
File Assignments:
| MDIN: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDOUT: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| INPCRD: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| PARM: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| RESTRT: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| REFC: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDVEL: mdvel
| MDEN: mden
| MDCRD: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
| MDINFO: /bgfs/jdurrant/amm503/oasci/metalflare/study/data/001-rogfp-md/simulat
|LOGFILE: logfile
| MDFRC: mdfrc
Then it will provide any notes and information about the chosen methods and system.
Afterwords, system information will be printed every
[ntpr][schemas.workflow.amber.inputs.AmberInputsBase.ntpr] steps.
NSTEP = 500 TIME(PS) = 1021.000 TEMP(K) = 300.64 PRESS = 0.0
Etot = -103950.9351 EKtot = 19726.5940 EPtot = -123677.5291
BOND = 650.1569 ANGLE = 1869.0536 DIHED = 1260.6252
UB = 0.0000 IMP = 0.0000 CMAP = 155.1250
1-4 NB = 787.8972 1-4 EEL = 10500.5192 VDWAALS = 18651.1452
EELEC = -157552.0512 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 317418.4248
Density = 1.0361
Ewald error estimate: 0.1408E-04
------------------------------------------------------------------------------
The meaning of each term is below for convenience. You can find more information in the Amber manual.
NSTEP: Current step number.TIME(PS): Cumulative simulation time in picoseconds. The previous simulation time is included here if the simulation is a restart.TEMP(K): Instantaneous system temperature in Kelvin.PRESS: System pressure.Etot: Total energy as the sum of kinetic and potential energies.EKtot: Total kinetic energy.EPtot: Total potential energy.BOND: Sum of bond energies.ANGLE: Sum of angle energies.DIHED: Sum of dihedral energies.UB: Urey-Bradley energy term in the CHARMM force field.IMP: Improper energy term as in the CHARMM force field.CMAP: Correction map for dihedral energies first introduced in CHARMM in the extended in Amber's ff19SB (replaces cosine-based \(\phi\)/\(\psi\) dihedral terms in ff14SB).1-4 NB: 1-4 non-bonded (i.e., van der Waal) energy between atoms separated by three consecutive bonds. These interactions scale unlike the standard terms, so they are treated separately.1-4 EEL: 1-4 electrostatic energy between atoms separated by three consecutive bonds. These interactions scale unlike the standard terms, so they are treated separately.VDWAALS: van der Waals energy.EELEC: Electrostatic energy.EHBOND: Depreciated hydrogen bonding contributions.RESTRAINT: Energy of anyntrconstraints.EKCMT: ?VIRIAL: ?VOLUME: System volume in Å3.Density: System density in g/cm3.
mdvel = None
¶
Sander option: -v
output velocity sets saved over trajectory
mtmd = None
¶
Sander option: -mtmd
input (optional) containing list of files and parameters for targeted MD to multiple targets
prmtop = 'mol.prmtop'
¶
Sander option: -p
Path to a file containing input molecular topology, force field, periodic box type, atom and residue names.
refc = None
¶
Sander option: -ref
input (optional) reference coords for position restraints; also used for targeted MD
restrt = None
¶
Sander option: -r
output final coordinates, velocity, and box dimensions if any - for restarting run
suffix = None
¶
Sander option: -suffix
output this string will be added to all unspecified output files that are printed (for multisander runs, it will append this suffix to all output files)
render(with_newlines=False)
¶
Render the bash command to run an Amber simulation.
AmberInputsBase
¶
Bases: BaseModel, YamlIO, Render
baroscalingdir = Field(default=0)
¶
Flag for pressure scaling direction control. Applicable when using Monte Carlo
barostat ([barostat][schemas.workflow.amber.inputs.AmberInputsBase.barostat]
is 2) with anisotropic pressure scaling
([ntp][schemas.workflow.amber.inputs.AmberInputsBase.ntp] is 2).
0
box size scales randomly (\(x\), \(y\) or \(z\)) each scaling step
1
box scales only along \(x\)-direction, dimensions along \(y\)-, \(z\)-axes are fixed
2
box scales only along \(y\)-direction, dimensions along \(x\)-, \(z\)-axes are fixed
3
box scales only along \(z\)-direction, dimensions along \(x\)-, \(y\)-axes are fixed
barostat = Field(default=1)
¶
Flag used to control which barostat is used to regulate the pressure during the simulation. The barostat setting determines how the simulation box's volume is adjusted to maintain the desired pressure. Choosing the right barostat is important for the accuracy and stability of the simulation.
1
Berendsen barostat. This method scales the box dimensions and atomic coordinates to achieve the desired pressure. It is simpler but can lead to less accurate pressure control and may not generate a true NPT ensemble.
2
Monte Carlo barostat. This method uses Monte Carlo moves to adjust the box volume and is generally more accurate for maintaining constant pressure. It provides better sampling of the NPT ensemble and is recommended for most simulations.
bellymask = Field(default='')
¶
String that specifies the moving atoms when
[ibelly][schemas.workflow.amber.inputs.AmberInputsBase.ibelly] is 1.
comp = Field(default=44.6, gt=0.0)
¶
Compressibility of the system when
[ntp][schemas.workflow.amber.inputs.AmberInputsBase.ntp] > 0 in units of
10-6 bar-1. 44.6` x 10-6 bar-1,
appropriate for water. This value is used in pressure regulation to account for the
compressibility of the solvent or system being simulated.
csurften = Field(default=0)
¶
Flag for constant surface tension dynamics.
0
No constant surface tension.
1
Constant surface tension with interfaces in the \(yz\) plane
2
Constant surface tension with interfaces in the \(xz\) plane
3
Constant surface tension with interfaces in the \(xy\) plane
cut = Field(default=8.0, gt=0.0)
¶
Specifies the nonbonded cutoff in Angstroms. This parameter sets the distance beyond which nonbonded interactions (such as van der Waals and electrostatic interactions) are not explicitly calculated.
For Particle Mesh Ewald (PME), this value limits the direct space sum. PME is a method used to compute long-range electrostatic interactions efficiently by splitting them into short-range (direct space) and long-range (reciprocal space) components. The cutoff distance specifies the range within which the direct space interactions are computed explicitly, while interactions beyond this distance are handled in reciprocal space.
8.0Å is commonly used in many simulations as a balance between accuracy and computational efficiency. It ensures that the majority of significant interactions are captured while keeping the computational cost manageable.10.0Å can provide improved accuracy, especially in systems where long-range interactions are important. However, it increases the computational load.
When using an implicit solvent model, the nonbonded cutoff should be set to
9999.0 Å, effectively making it infinite. This is because implicit solvent models
treat solvation effects as a continuous medium, and all interactions need to be
considered without a cutoff.
drms = Field(default=0.0001, gt=0)
¶
The convergence criterion for the energy Derivative: minimization will halt when the Root-Mean-Square of the Cartesian elements of the gradient of the energy is less than this.
dt = Field(default=0.001, gt=0.0)
¶
The time step in picoseconds. This parameter defines the interval of time between each step in the simulation.
- With SHAKE
([
ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc] is2): The maximum value is0.002ps (2 fs). SHAKE constrains bond lengths involving hydrogen atoms, allowing for a larger time step. - Without SHAKE: The maximum value is
0.001ps (1 fs). Without bond constraints, a smaller time step is needed to maintain numerical stability.
Since longer simulations are usually desired, the maximum value is typically used. However, values lower than the maximum can be used if necessary for the phenomena of interest, such as high-frequency motions or other specific needs.
The use of Hydrogen Mass Repartitioning (HMR) together with SHAKE, allows the time
step to be increased in a stable fashion by about a factor of two (up to 0.004)
by slowing down the high frequency hydrogen motion in the system.
To use HMR, the masses in the topology file need to be altered before starting
the simulation. ParmEd can do this automatically with the HMassRepartition option.
tip
Consider the nature of your simulation; if capturing high-frequency motions is critical, a smaller time step might be required.
dx0 = Field(default=0.01, ge=0.0)
¶
The initial step length. If the initial step length is too big then will give a huge energy; however the minimizer is smart enough to adjust itself.
gamma_ln = Field(default=2.0, gt=0.0)
¶
The collision frequency, \(\gamma\), when
[ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 3. This parameter
is used in Langevin dynamics to control the rate of coupling between the system
and a heat bath, thereby regulating the temperature.
The default value is set to 2.0 ps-1, which is commonly used in many
simulations to provide effective temperature control without overly damping the
system's dynamics. Values typically range from 2.0 to 5.0 ps-1.
While the physical collision frequency is about 50 ps-1, using such
high values can overly dampen the system. Smaller values are preferred to maintain
more realistic dynamics.
gamma_ten = Field(default=0.0, ge=0.0)
¶
Surface tension value in units of dyne/cm.
ibelly = Field(default=0)
¶
Flag for belly type dynamics. If set to 1, a subset of the atoms in the system
will be allowed to move, and the coordinates of the rest will be frozen.
The moving atoms are specified with
[bellymask][schemas.workflow.amber.inputs.AmberInputsBase.bellymask].
This option is not available when
igb > 0. When belly
type dynamics is in use, bonded energy terms, vdW interactions, and direct
space electrostatic interactions are not calculated for pairs of frozen atoms.
Note that this does not provide any significant speed advantage. Freezing
atoms can be useful for some applications but is maintained primarily for
backwards compatibility with older versions of Amber. Most applications should
use the [ntr][schemas.workflow.amber.inputs.AmberInputsBase.ntr] variable
instead to restrain parts of the system to stay close to some initial configuration.
idecomp = Field(default=0)
¶
Perform energy decomposition according to a chosen scheme. In former
distributions this option was only really useful in conjunction with mm_pbsa,
where it is turned on automatically if required. Now, a
decomposition of \(\left\langle \partial V / \partial \gamma \right\rangle\) on a
per-residue basis in thermodynamic integration (TI) simulations is also possible.
If energy decomposition is requested, residues may be chosen by the RRES and/or LRES card. The RES card is used to select the residues about which information is written out.
0
Do not decompose energies.
1
Decompose energies on a per-residue basis; 1-4 EEL + 1-4 VDW are added to internal (bond, angle, dihedral) energies.
2
Decompose energies on a per-residue basis; 1-4 EEL + 1-4 VDW are added to EEL and VDW.
3
Decompose energies on a pairwise per-residue basis; otherwise equivalent to
[idecomp][schemas.workflow.amber.inputs.AmberInputsBase.idecomp] is 1.
Not available in TI simulations.
4
Decompose energies on a pairwise per-residue basis; otherwise equivalent to
[idecomp][schemas.workflow.amber.inputs.AmberInputsBase.idecomp] is 2.
Not available in TI simulations.
ig = Field(default=-1)
¶
The seed for the pseudo-random number generator. This affects the starting velocities
for MD simulations if
[tempi][schemas.workflow.amber.inputs.AmberInputsBase.tempi] is nonzero.
If this is -1, a random seed will be computed based on the current date and time.
This should almost always be -1 unless you are reproducing a run.
tip
- Set to
-1to ensure that each simulation run starts with a different seed, providing varied initial conditions for better sampling. - Use a specific integer value if you need to reproduce an exact simulation run for debugging or verification purposes.
- Ensure that [
tempi][schemas.workflow.amber.inputs.AmberInputsBase.tempi] is set appropriately when using this option to affect starting velocities.
imin = Field(default=0)
¶
Flag for running the energy minimization procedure.
0
Run molecular dynamics without any minimization.
Perform molecular dynamics (MD) simulation. This mode generates configurations by integrating Newtonian equations of motion, allowing the system to sample more configurational space and cross small potential energy barriers.
1
Perform energy minimization.
This mode iteratively moves the atoms down the energy gradient to relax the structure until a sufficiently low average gradient is obtained. Minimization is useful for preparing a system before MD simulations to remove bad contacts and high-energy configurations.
5
Read in a trajectory for analysis using the minimization algorithms.
Although sander will write energy information in the output files
(using [ntpr][schemas.workflow.amber.inputs.AmberInputsBase.ntpr]),
it is often desirable to calculate the energies of a set of structures at a
later point. In particular, one may wish to post-process a set of structures using
a different energy function than was used to generate the structures.
An example of this is MM-PBSA analysis, where the explicit water is removed and
replaced with a continuum model.
If [imin][schemas.workflow.amber.inputs.AmberInputsBase.imin] is set to
5, sander will read a trajectory file (the inptraj argument, specified using
-y on the command line), and will perform the functions described in the mdin
file (e.g., an energy minimization) for each of the structures in this file.
The final structure from each minimization will be written out to the normal
mdcrd file. If you wish to read in a binary (i.e., NetCDF format) trajectory,
be sure to set [ioutfm][schemas.workflow.amber.inputs.AmberInputsBase.ioutfm]
to 1. Note that this will result in the output trajectory having NetCDF format
as well.
For example, when [imin][schemas.workflow.amber.inputs.AmberInputsBase.imin]
is 5 and [maxcyc][schemas.workflow.amber.inputs.AmberInputsBase.maxcyc] is
1000, sander will minimize each structure in the trajectory for 1000 steps and
write a minimized coordinate set for each frame to the mdcrd file.
If [maxcyc][schemas.workflow.amber.inputs.AmberInputsBase.maxcyc] is 1, the
output file can be used to extract the energies of each of the coordinate
sets in the inptraj file.
Trajectories containing box coordinates can be post-processed. In order to read
trajectories with box coordinates,
[ntb][schemas.workflow.amber.inputs.AmberInputsBase.ntb] should be greater
than 0.
6
Read in a trajectory for analysis using the molecular dynamics driver.
Like when [imin][schemas.workflow.amber.inputs.AmberInputsBase.imin] is 5,
this option reads a trajectory file for analysis (the inptraj argument,
specified using -y on the command line). Instead of minimizing the potential
energy of each coordinate set, it instead initiates dynamics from each frame as
if it were read as a restart file without initial velocities. That is, this
option is equivalent to outputting each frame as a restart file and starting the
dynamics with [irest][schemas.workflow.amber.inputs.AmberInputsBase.irest]
is 0. If [nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim] is
0, then this effectively performs a single point energy for each frame.
7
Listen to the selected internet socket and return energies and forces when instructed by an external server.
When this option is set, sander does not perform MD; instead, it listens
for messages from a server instructing it to compute the potential energy and
forces of a system. The server IP address and port number are provided as command
line arguments -host and -port. The default values are -host 127.0.0.1 and
-port 31415. The communication pattern follows the protocol implemented in the
i-PI software. The i-PI program is a molecular dynamics driver used to perform
classical and centroid path integral molecular dynamics. When i-PI performs
classical MD, one can instantiate a single sander process to evaluate the
potential. However, when i-PI is used to perform PIMD, which involves
calculating potential energies for several “beads” at each time step, multiple
instances of sander can be launched to simultaneously evaluate the required
potential energies. The current implementation of the interface is limited to
simulations in the NVE an NVT ensembles; therefore, one should launch sander with
a restart file whose unit cell lattice vectors are consistent with the input
structure supplied to i-PI.
ionstepvelocities = Field(default=0)
¶
Controls whether to print the half-step-ahead velocities (0) or
on-step velocities (1). The half-step-ahead velocities can potentially
be used to restart calculations, but the on-step velocities correspond to
calculated kinetic energy/temperature.
ioutfm = Field(default=1)
¶
Format of coordinate and velocity trajectory files.
0
ASCII.
1
Binary NetCDF files.
irest = Field(default=0)
¶
Flag to restart a simulation from a previously saved restart file. Restarting a simulation can help in managing large simulations by breaking them into smaller, manageable segments and allows for continued simulation from the point of interruption without losing progress.
0
Do not restart the simulation; instead, run as a new simulation. Velocities in the
input coordinate file, if any, will be ignored, and the time step count will be set
to 0 (unless overridden by
[t][schemas.workflow.amber.inputs.AmberInputsBase.t]).
1
Restart the simulation, reading coordinates and velocities from a previously saved
restart file. The velocity information is necessary when restarting, so
[ntx][schemas.workflow.amber.inputs.AmberInputsBase.ntx] must be
5 (for Amber versions much older than 20,
[ntx][schemas.workflow.amber.inputs.AmberInputsBase.ntx] must be greater than
or equal to 4),
if [irest][schemas.workflow.amber.inputs.AmberInputsBase.irest] is 1.
iwrap = Field(default=0)
¶
Flag for wrapping coordinates around the periodic boundary.
0
No wrapping will be performed, in which case it is typical to use cpptraj as a post-processing program to translate molecules back to the primary box.
1
The coordinates written to the restart and trajectory files will be "wrapped" into a primary box. This means that for each molecule, its periodic image closest to the middle of the "primary box" (with \(x\) coordinates between \(0\) and \(a\), \(y\) coordinates between \(0\) and \(b\), and \(z\) coordinates between \(0\) and \(c\)) will be the one written to the output file. This often makes the resulting structures look better visually, but has no effect on the energy or forces. Performing such wrapping, however, can mess up diffusion and other calculations.
For very long runs, setting
[iwrap][schemas.workflow.amber.inputs.AmberInputsBase.iwrap] is 1 may be
required to keep the coordinate output from overflowing the trajectory and
restart file formats, especially if trajectories are written in ASCII format
instead of NetCDF (see also the
[ioutfm][schemas.workflow.amber.inputs.AmberInputsBase.ioutfm] option).
jfastw = Field(default=0)
¶
Fast water definition flag. By default, the system is searched for water residues, and special routines are used to SHAKE these systems.
0
Waters are identified by the default names, unless they are redefined, as described below.
4
Do not use the fast SHAKE routines for waters.
Info
The following variables allow redefinition of the default residue and atom names used by the program to determine which residues are waters.
WATNAMThe residue name the program expects for water. DefaultWAT.OWTNMThe atom name the program expects for the oxygen of water. DefaultO.HWTNM1The atom name the program expects for the 1st H of water. DefaultH1.HWTNM2The atom name the program expects for the 2nd H of water. DefaultH2.
maxcyc = Field(default=9999, ge=1)
¶
Maximum number of minimization cycles allowed. This parameter sets the upper limit
on the number of cycles the minimization algorithm will perform.
Values typically range from 1000 to 50000. Lower values may be sufficient for
small systems or those close to their minimum energy state, while larger values
can help ensure convergence in more complex or strained systems.
tip
- If the system is large or highly strained, consider increasing the value to ensure sufficient minimization.
- For smaller or well-equilibrated systems, a lower value might be adequate, saving computational resources.
- Monitor the energy convergence; if the energy stabilizes before reaching
maxcyc, the minimization can be considered complete.
mcbarint = Field(default=100, ge=1)
¶
Number of steps between volume change attempts performed as part of the Monte Carlo barostat. This determines how frequently the volume of the simulation box is adjusted during pressure regulation.
ncyc = Field(default=10, ge=1)
¶
If [ntmin][schemas.workflow.amber.inputs.AmberInputsBase.ntmin] is 1,
then the minimization method will be switched from steepest descent
to conjugate gradient after
[ncyc][schemas.workflow.amber.inputs.AmberInputsBase.ncyc] cycles.
Values typically range from 5 to 100.
Lower values will switch to conjugate gradient sooner, which can be more efficient
for systems nearing their minimum energy state. Higher values will keep the
minimization in steepest descent mode longer, which can be beneficial for systems
far from equilibrium. The default value is set to 10, which provides a balance
between the robustness of steepest descent and the efficiency of conjugate gradient
methods.
tip
- Adjust the value based on the size and complexity of your system. For larger or more complex systems, a higher value might be necessary to ensure sufficient initial minimization.
- For systems that are relatively close to their equilibrium state, a lower value may expedite the minimization process by switching to the more efficient conjugate gradient method sooner.
- Monitor the minimization process; if convergence is slow, consider
increasing
ncycto allow more initial steepest descent cycles.
ninterface = Field(default=2, ge=2, le=9)
¶
Number of interfaces in the periodic box. There must be at least two interfaces in the periodic box. Two interfaces is appropriate for a lipid bilayer system and is the default value.
nkija = Field(default=1, ge=1)
¶
For use with [ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] if 9 or 10.
For [ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 9, this the
number of substeps of [dt][schemas.workflow.amber.inputs.AmberInputsBase.dt]
when integrating the thermostat equations of motion, for greater accuracy.
For [ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 10, this
specifies the number of additional auxiliary velocity variables v1 and v2, which
will total nkija \(\times\) v1 + nkija \(\times\) v2
nmropt = Field(default=0)
¶
0
No nmr-type analysis will be done.
1
NMR restraints and weight changes will be read.
2
NMR restraints, weight changes, NOESY volumes, chemical shifts and residual dipolar restraints will be read.
noshakemask = Field(default='')
¶
String that specifies atoms that are not to be shaken
(assuming that [ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc]>1).
Any bond that would otherwise be shaken by virtue of the
[ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc] flag, but which
involves an atom flagged here, will not be shaken.
Default is an empty string, which matches nothing. A typical use would be to remove
SHAKE constraints from all or part of a solute, while still shaking rigid water
models like TIPnP or SPC/E. Another use would be to turn off SHAKE constraints for
the parts of the system that are being changed with thermodynamic integration, or
which are the EVB or quantum regions of the system.
If this option is invoked, then all parts of the potential must be evaluated,
that is, [ntf][schemas.workflow.amber.inputs.AmberInputsBase.ntf] must be 1.
The code enforces this by setting
[ntf][schemas.workflow.amber.inputs.AmberInputsBase.ntf] to 1 when a
noshakemask string is present in the input.
If you want the noshakemask to apply to all or part of the water molecules,
you must also set
[jfastw][schemas.workflow.amber.inputs.AmberInputsBase.jfastw] to 4, to turn
off the special code for water SHAKE. (If you are not shaking waters, you
presumably also want to issue the "set default FlexibleWater on" command in LEaP;
see that chapter for more information.)
nrespa = Field(default=1, ge=1)
¶
This variable allows the user to evaluate slowly-varying terms in the force field less frequently. For PME, "slowly-varying" (now) means the reciprocal sum. For generalized Born runs, the "slowly-varying" forces are those involving derivatives with respect to the effective radii, and pair interactions whose distances are greater than the "inner" cutoff, currently hard-wired at 8 Å.
If [nrespa][schemas.workflow.amber.inputs.AmberInputsBase.nrespa] > 1
these slowly-varying forces are evaluated every
[nrespa][schemas.workflow.amber.inputs.AmberInputsBase.nrespa] steps.
The forces are adjusted appropriately, leading to an impulse at that step.
If [nrespa][schemas.workflow.amber.inputs.AmberInputsBase.nrespa]
\(\times\) [dt][schemas.workflow.amber.inputs.AmberInputsBase.dt]
is less than or equal to 4 fs then the energy conservation is not seriously
compromised. However if
[nrespa][schemas.workflow.amber.inputs.AmberInputsBase.nrespa] \(\times\)
[dt][schemas.workflow.amber.inputs.AmberInputsBase.dt] > 4 fs then the
simulation becomes less stable. Note that energies and related quantities are
only accessible every
[nrespa][schemas.workflow.amber.inputs.AmberInputsBase.nrespa] steps, since
the values at other times are meaningless.
nscm = Field(default=1000, ge=1)
¶
Flag for the removal of translational and rotational center-of-mass motion every
[nscm][schemas.workflow.amber.inputs.AmberInputsBase.nscm] steps.
For periodic simulations
([ntb][schemas.workflow.amber.inputs.AmberInputsBase.ntb] is 1 or 2),
only the translational center-of-mass motion is removed.
Reasonable values are between 100 and 2000. Lower values ensure
more frequent removal of center-of-mass motion, which can be beneficial
for stability in certain simulations.
tip
- Use lower values (closer to
100) for systems that may experience significant drift or when higher precision is required. - Higher values (up to
2000) can be used for more stable systems or to reduce computational overhead in very long simulations. - Monitor the simulation to ensure that the chosen value effectively manages the center-of-mass motion without introducing artifacts or instability.
nstlim = Field(default=1, ge=1)
¶
Number of MD steps to perform. Multiply
[nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim] and
[dt][schemas.workflow.amber.inputs.AmberInputsBase.dt] to get the duration
of the MD simulation in picoseconds.
tip
- For short equilibration runs or quick tests, use lower values of
[
nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim], such as5000to50000. - For production runs aimed at sampling equilibrium states or studying
slower processes, higher values of
[
nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim] are recommended, typically in the range of1000000to50000000(corresponding to 2 ns to 100 ns fordt = 0.002). - Adjust [
nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim] based on the specific requirements of your study, considering both the computational resources available and the timescale of the phenomena you are investigating.
ntave = Field(default=0, ge=0.0)
¶
Every [ntave][schemas.workflow.amber.inputs.AmberInputsBase.ntave] steps of
dynamics, running averages of average energies and fluctuations over the last
[ntave][schemas.workflow.amber.inputs.AmberInputsBase.ntave] steps will be
printed out. A value of 0 disables this printout. Setting
[ntave][schemas.workflow.amber.inputs.AmberInputsBase.ntave] to a value
½ or ¼ of nstlim provides a simple way to look at convergence during the
simulation.
ntb = Field(default=1)
¶
Flag for periodic boundary conditions when computing non-bonded interactions. Bonds that cross the boundary are not supported.
0
No periodic boundary conditions. This is suitable for simulations where boundary effects are not a concern, such as in isolated systems or gas-phase simulations.
1
Constant volume. This maintains a fixed simulation box size, appropriate for systems where volume changes are not expected or desired.
2
Constant pressure. This allows the simulation box to fluctuate in size to maintain constant pressure, suitable for more realistic simulations of condensed-phase systems where pressure control is needed.
ntc = Field(default=1)
¶
Flag for SHAKE to perform bond length constraints. The SHAKE option should be used
for most MD calculations. The size of the MD timestep is determined by the
fastest motions in the system. SHAKE removes the bond stretching freedom, which
is the fastest motion, and consequently allows a larger timestep to be used.
For water models, a special "three-point" algorithm is used. Consequently, to
employ TIP3P set [ntf][schemas.workflow.amber.inputs.AmberInputsBase.ntf] and
[ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc] to 2.
Since SHAKE is an algorithm based on dynamics, the minimizer is not aware of what SHAKE is doing; for this reason, minimizations generally should be carried out without SHAKE. One exception is short minimizations whose purpose is to remove bad contacts before dynamics can begin.
For parallel versions of sander only intramolecular atoms can be constrained. Thus, such atoms must be in the same chain of the originating PDB file.
1
No SHAKE. This option does not apply any bond length constraints and is required for minimization.
2
Bonds involving hydrogen are constrained. This is the recommended setting for molecular dynamics (MD) simulations as it allows for larger time steps while maintaining stability.
3
All bonds are constrained. This setting applies constraints to all bonds, providing the most rigid structure.
Warning
Not available for parallel or qmmm runs in sander.
ntf = Field(default=1)
¶
Force evaluation type. This parameter determines which interactions are considered during the force calculations.
1
All contributions. This option includes all types of interactions in the force evaluation and is required for minimization.
2
Ignore bond interactions involving hydrogens. This option is typically used when
[ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc] is 2, meaning
constraints are applied to bonds involving hydrogens (e.g., SHAKE algorithm).
3
All bond interactions are omitted. This option is used when
[ntc][schemas.workflow.amber.inputs.AmberInputsBase.ntc] is 3, which
implies constraints are applied to all bonds.
4
angle involving H-atoms and all bonds are omitted
5
all bond and angle interactions are omitted
6
dihedrals involving H-atoms and all bonds and all angle interactions are omitted
7
all bond, angle and dihedral interactions are omitted
8
all bond, angle, dihedral and non-bonded interactions are omitted
ntmin = Field(default=1)
¶
Flag for selecting minimization type. Determines the algorithm used for energy minimization.
0
Full conjugate gradient minimization. The first four cycles are steepest descent at the start of the run and after every nonbonded pair list update. Conjugate gradient is slower than steepest descent when far from a minimum but becomes more efficient when close to the minimum.
1
For [ncyc][schemas.workflow.amber.inputs.AmberInputsBase.ncyc] cycles, the
steepest descent method is used, then the conjugate gradient is switched on.
This option combines the robustness of steepest descent with the efficiency of
conjugate gradient, making it a recommended choice for many scenarios.
2
Only the steepest descent method is used. This algorithm is popular because it is robust and easy to implement. It is generally effective for systems far from equilibrium.
3
The XMIN method is used. This method leverages advanced optimization algorithms for more efficient minimization, especially useful for large or complex systems.
4
The LMOD method is used. This approach uses Low-Mode Conformational Search combined with XMIN for energy relaxation and minimization, particularly effective for exploring conformational space in flexible molecules.
ntp = Field(default=0)
¶
Flag for constant pressure dynamics. This parameter controls how pressure is managed during the simulation.
0
No pressure scaling. The system is run at constant volume, and no adjustments are made to maintain a specific pressure.
1
Isotropic position scaling. This is the recommended setting for most simulations as it scales the simulation box uniformly in all directions to maintain constant pressure.
2
Anisotropic pressure scaling. This option allows different scaling factors for each dimension and can only be used for orthogonal boxes. It is typically used in membrane simulations where different surface tensions exist in the \(x\), \(y\), and \(z\) directions. Solutes dissolved in water should not use this setting as it can introduce artifacts.
3
Molecular dynamics with semiisotropic pressure scaling: this is only available with
constant surface tension (csurften > 0) and orthogonal boxes. This links the
pressure coupling in the two directions tangential to the interface.
4
Molecular dynamics towards a targeted volume. This is not for production but
for modifying the volume of the system, particularly useful for preparing
replica-exchange molecular dynamics simulations where the shape of each replica
needs to be the same. When
[ntp][schemas.workflow.amber.inputs.AmberInputsBase.ntp] is 4, the following
variables in the “ewald” namelist should be set:
target_n: Number of target volume iterations to reach the target volume (default 100).target_a,target_b,target_c: the cell dimension of the target volume.
ntpr = Field(default=1000, ge=1)
¶
Print energy information every
[ntpr][schemas.workflow.amber.inputs.AmberInputsBase.ntpr] steps in a
human-readable form to files mdout and mdinfo. mdinfo is closed and
reopened each time, so it always contains the most recent energy and temperature.
ntr = Field(default=0)
¶
Flag for restraining positions of specified atoms using a harmonic potential.
Ensure that
[restraintmask][schemas.workflow.amber.inputs.AmberInputsBase.restraintmask]
is properly defined to specify the atoms that require constraints.
0
No constraints. The positions of all atoms are free to move according to the
simulation dynamics. Use 0 for fully flexible simulations where no positional
restraints are needed.
1
Constrain atoms specified in
[restraintmask][schemas.workflow.amber.inputs.AmberInputsBase.restraintmask].
This applies a harmonic potential to the atoms defined in
[restraintmask][schemas.workflow.amber.inputs.AmberInputsBase.restraintmask],
effectively fixing their positions relative to the rest of the system.
Use 1 when specific atoms need to be restrained, such as in cases where you want
to focus on a particular region of the system while keeping another region fixed
or minimally perturbed.
ntt = Field(default=3)
¶
Switch for temperature scaling.
0
Constant total energy (NVE).
1
Constant temperature, using the weak-coupling algorithm. A single scaling factor is used for all atoms. Note that this algorithm just ensures that the total kinetic energy is appropriate for the desired temperature; it does nothing to ensure that the temperature is even over all parts of the molecule. Atomic collisions will tend to ensure an even temperature distribution, but this is not guaranteed, and there are many subtle problems that can arise with weak temperature coupling.
Using [ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] of 1 is
especially dangerous for generalized Born simulations, where there are no
collisions with solvent to aid in thermalization.
Other temperature coupling options (especially
[ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] of 3) should be
used instead.
2
Andersen-like temperature coupling scheme, in which imaginary "collisions"
are performed with heat bath of temperature
[temp0][schemas.workflow.amber.inputs.AmberInputsBase.temp0] every
[vrand][schemas.workflow.amber.inputs.AmberInputsBase.vrand] steps.
note
In between these "massive collisions", the dynamics is Newtonian. Hence, time correlation functions (etc.) can be computed in these sections, and the results averaged over an initial canonical distribution. Note also that too high a collision rate (too small a value of vrand) will slow down the speed at which the molecules explore configuration space, whereas too low a rate means that the canonical distribution of energies will be sampled slowly.
3
Use Langevin dynamics with the collision frequency
[gamma_ln][schemas.workflow.amber.inputs.AmberInputsBase.gamma_ln].
Since Langevin simulations are highly susceptible to "synchronization"
artifacts, you should explicitly set
[ig][schemas.workflow.amber.inputs.AmberInputsBase.ig] to a different value
every restart (e.g., -1).
9
Optimized Isokinetic Nose-Hoover chain ensemble (OIN). Constant temperature simulation utilizing Nose-Hoover chains and an isokinetic constraint on the particle and thermostat velocities, implemented for use in multiple time-stepping methods, namely for 3D-RISM and RESPA.
10
Stochastic Isokinetic Nose-Hoover RESPA integrator. Mainly used for RESPA simulations.
11
Stochastic version of Berendsen thermostat, also known as the Bussi thermostat. This thermostat samples canonical distribution by scaling all velocities to a random temperature probed from canonical distribution.
ntwe = Field(default=0, ge=0)
¶
Every [ntwe][schemas.workflow.amber.inputs.AmberInputsBase.ntwe] steps,
the energies and temperatures will be written to file mden in a compact form. If
[ntwe][schemas.workflow.amber.inputs.AmberInputsBase.ntwe] is 0 then no
mden file will be written. Note that energies in the mden file are not
synchronized with coordinates or velocities in the mdcrd or mdvel file(s).
Assuming identical [ntwe][schemas.workflow.amber.inputs.AmberInputsBase.ntwe]
and [ntwx][schemas.workflow.amber.inputs.AmberInputsBase.ntwx] values the
energies are one time step before the coordinates (as well as the velocities
which are synchronized with the coordinates). Consequently, an mden file is
rarely written.
ntwf = Field(default=0, ge=0)
¶
Every [ntwf][schemas.workflow.amber.inputs.AmberInputsBase.ntwf] steps, the
forces will be written to the mdfrc file. If
[ntwf][schemas.workflow.amber.inputs.AmberInputsBase.ntwf] is 0, no force
trajectory file will be written. If
[ntwf][schemas.workflow.amber.inputs.AmberInputsBase.ntwf] is -1, forces
will be written to the mdcrd, which then becomes a combind coordinate/force
trajectory file, at the interval defined by
[ntwx][schemas.workflow.amber.inputs.AmberInputsBase.ntwx].
This option is available only for binary NetCDF output
([ioutfm][schemas.workflow.amber.inputs.AmberInputsBase.ioutfm] is 1).
Most users will have no need for a force trajectory file and so can safely
leave [ntwf][schemas.workflow.amber.inputs.AmberInputsBase.ntwf] at the default.
Note that dumping forces frequently, like velocities or coordinates, will introduce
potentially significant I/O and communication overhead, hurting both performance
and parallel scaling.
ntwprt = Field(default=0, ge=0)
¶
The number of atoms to include in trajectory files (mdcrd and mdvel).
This flag can be used to decrease the size of the these files, by including only
the first part of the system, which is usually of greater interest (for instance,
one might include only the solute and not the solvent).
0
Include all atoms of the system when writing trajectories.
> 0
Include only atoms 1 to
[ntwprt][schemas.workflow.amber.inputs.AmberInputsBase.ntwprt] when writing
trajectories.
ntwr = Field(default=1000, ge=1)
¶
Every [ntwr][schemas.workflow.amber.inputs.AmberInputsBase.ntwr] steps
during dynamics, the restrt file will be written, ensuring that recovery from a
crash will not be so painful. No matter what the value of
[ntwr][schemas.workflow.amber.inputs.AmberInputsBase.ntwr], a restrt file
will be written at the end of the run, i.e., after
[nstlim][schemas.workflow.amber.inputs.AmberInputsBase.nstlim] steps
(for dynamics) or
[maxcyc][schemas.workflow.amber.inputs.AmberInputsBase.maxcyc] steps
(for minimization). If
[ntwr][schemas.workflow.amber.inputs.AmberInputsBase.ntwr] < 0, a unique
copy of the file, restrt_<nstep>, is written every abs(ntwr) steps.
This option is useful if for example one wants to run free energy perturbations
from multiple starting points or save a series of restrt files for minimization.
ntwv = Field(default=0, ge=0.0)
¶
Every [ntwv][schemas.workflow.amber.inputs.AmberInputsBase.ntwv] steps,
the velocities will be written to the mdvel file. If
[ntwv][schemas.workflow.amber.inputs.AmberInputsBase.ntwv] is 0, no
velocity trajectory file will be written. If
[ntwv][schemas.workflow.amber.inputs.AmberInputsBase.ntwv] is -1, velocities
will be written to mdcrd, which then becomes a combined coordinate/velocity
trajectory file, at the interval defined by ntwx. This option is available
only for binary NetCDF output
([ioutfm][schemas.workflow.amber.inputs.AmberInputsBase.ioutfm] is 1).
Most users will have no need for a velocity trajectory file and so can safely
leave [ntwv][schemas.workflow.amber.inputs.AmberInputsBase.ntwv] at the default.
Note that dumping velocities frequently, like forces or coordinates, will introduce
potentially significant I/O and communication overhead, hurting both performance
and parallel scaling.
ntwx = Field(default=0, ge=1)
¶
Coordinates are written every
[ntwx][schemas.workflow.amber.inputs.AmberInputsBase.ntwx] steps to the
mdcrd file. This parameter controls how often the coordinates are saved,
which can be used for trajectory analysis. If
[ntwx][schemas.workflow.amber.inputs.AmberInputsBase.ntwx] is 0, no coordinate
trajectory file will be written.
ntx = Field(default=1)
¶
Option to read the initial coordinates, velocities, and box size from the inpcrd file.
1
File is read with no initial velocity information. Suitable for
starting simulations with new systems where velocities are generated based
on [tempi][schemas.workflow.amber.inputs.AmberInputsBase.tempi]
Option 1 must be used when one is starting from minimized or model-built
coordinates.
5
File is read unformatted with no initial velocity information. This is less common and mainly used for specific needs when dealing with unformatted coordinate files.
If an MD restrt file is specified for inpcrd then option 5 is generally used
(unless you explicitly wish to ignore the velocities that are present).
ntxo = Field(default=2)
¶
Format of the final coordinates, velocities, and box size (if a constant volume or
pressure run) written to file restrt.
1
ASCII.
2
Binary NetCDF file.
pres0 = Field(default=1.0, gt=0.0)
¶
Reference pressure, in bar, at which the system is maintained. This is the target pressure for the barostat. This value is almost always used in simulations to mimic standard atmospheric conditions.
restraint_wt = Field(default=4.0, ge=0.0)
¶
The weight (in kcal mol-1 Å-2) when
[ntr][schemas.workflow.amber.inputs.AmberInputsBase.ntr] is 1. The form of
the restraint is
\(k (\Delta x)^2\) where \(\Delta x\) is the deviation of the atom's coordinate
from the reference position.
- Reasonable values are between
0.1and10.0.- Lower values (
0.1to1.0) allow for more movement, providing a looser restraint. - Higher values (
5.0to10.0) significantly restrict movement, enforcing a tighter restraint.
- Lower values (
- The default value is set to
4.0, which provides a moderate restraint, balancing stability and flexibility.
restraintmask = Field(default='')
¶
Strings that specify the restricted atoms when
[ntr][schemas.workflow.amber.inputs.AmberInputsBase.ntr] is 1. To see what
atoms will be restrained, you can use
ambmask -p mol.prmtop -c mol.inpcrd -out pdb -find "RESTRAINT_STRING"
in ambertools. Here are some examples of restraintmasks and their descriptions.
"!(@H=)": Restrain all atoms except hydrogens."!(:WAT) & !(@H=)": Restrain all atoms except hydrogens and water molecules."!(:WAT) & !(@H=) & !(:Na+,Cl-)": Same as above, but does not restrain Na+ and Cl- ions."!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')": Restrains protein, DNA, and RNA backbone atoms.
We must include the !(:WAT) to avoid restraining oxygen atoms in the water molecules.
sinrtau = Field(default=1.0, gt=0.0)
¶
For the SINR (Stochastic Isokinetic Nose-Hoover RESPA) integrator
([ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 10), this
specifies the time scale for determining the masses associated with the two
auxiliary velocity variables v1 and v2 (e.g. thermostat velocities) and hence
the magnitude of the coupling of the physical velocities with the auxiliary
velocities. Generally this should be related to the time scale of the system.
t = Field(default=0.0, ge=0.0)
¶
The time at the start (psec) this is for your own reference and is not critical.
Start time is taken from the coordinate input file if
[irest][schemas.workflow.amber.inputs.AmberInputsBase.irest] is 1.
taup = Field(default=1.0, gt=0.0)
¶
Pressure relaxation time in picoseconds when
[ntp][schemas.workflow.amber.inputs.AmberInputsBase.ntp] > 0.
Recommended values are between 1.0 and 5.0 ps. This parameter controls how
quickly the pressure adjusts to the target value. Start with 1.0 ps.
If your simulations are unstable, consider increasing this value.
tautp = Field(default=1.0, gt=0)
¶
Time constant, in ps, for heat bath coupling for the system, if
[ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 1.
Generally, values for
[tautp][schemas.workflow.amber.inputs.AmberInputsBase.tautp] should be in the
range of 0.5 to 5.0 ps, with a smaller value providing tighter coupling to the
heat bath and, thus, faster heating and a less natural trajectory. Smaller values of
[tautp][schemas.workflow.amber.inputs.AmberInputsBase.tautp] result in
smaller fluctuations in kinetic energy, but larger fluctuations in the total energy.
Values much larger than the length of the simulation result in a return
to constant energy conditions.
temp0 = Field(default=300.0, gt=0.0)
¶
Reference temperature at which the system will be kept in Kelvin. This parameter defines the target temperature for the simulation, around which the thermostat will regulate the system. It is crucial for simulations where temperature control is needed to mimic real-world conditions, such as simulations of biological systems or materials at specific temperatures.
The default value is set to 300.0 K, which corresponds to approximately room
temperature. This is a common target temperature for many biological simulations.
Other typical values might include 310.0 K for physiological conditions
(human body temperature) or other specific temperatures relevant to your study.
temp0les = Field(default=-1, ge=-1)
¶
This is the target temperature for all LES particles. If
[temp0les][schemas.workflow.amber.inputs.AmberInputsBase.temp0les] < 0,
a single temperature bath is used for all atoms, otherwise separate thermostats
are used for LES and non-LES particles. Default is -1, corresponding to a single
(weak-coupling) temperature bath.
tempi = Field(default=100.0, gt=0.0)
¶
Initialization temperature in Kelvin. This parameter sets the initial temperature for the system at the start of the simulation.
- If [
ntx][schemas.workflow.amber.inputs.AmberInputsBase.ntx] is1, the initial velocities of the atoms are assigned from a Maxwellian distribution corresponding to the temperature [tempi][schemas.workflow.amber.inputs.AmberInputsBase.tempi]. This is typically used to start a new simulation where the initial conditions need to be defined. - If [
ntx][schemas.workflow.amber.inputs.AmberInputsBase.ntx] is5, this parameter has no effect because the velocities are read from the input coordinates file, meaning the system continues from a previously equilibrated state.
tip
Use a lower initial temperature (e.g., 100.0 K) to gradually equilibrate
the system and avoid potential instabilities or large initial forces.
tol = Field(default=1e-05, gt=0.0)
¶
Relative geometrical tolerance for coordinate resetting in shake.
Recommended maximum: < 0.00005 Angstroms.
vlimit = Field(default=20.0, ge=0.0)
¶
If not equal to 0.0, then any component of the velocity that is greater than
abs(VLIMIT) will be reduced to VLIMIT (preserving the sign). This can be used to
avoid occasional instabilities in molecular dynamics runs. VLIMIT should
generally be set to a value like 20 (the default), which is well above the most
probable velocity in a Maxwell-Boltzmann distribution at room temperature.
A warning message will be printed whenever the velocities are modified.
Runs that have more than a few such warnings should be carefully examined.
vrand = Field(default=1000, ge=1)
¶
If [vrand][schemas.workflow.amber.inputs.AmberInputsBase.vrand] > 0
and [ntt][schemas.workflow.amber.inputs.AmberInputsBase.ntt] is 2, the
velocities will be randomized to temperature
[temp0][schemas.workflow.amber.inputs.AmberInputsBase.temp0] every
[vrand][schemas.workflow.amber.inputs.AmberInputsBase.vrand] steps.
render(with_newlines=False)
¶
Render AMBER input file.