Simulation control options
An example of how config file of simulation looks like.
[OPTIONS]
md_steps = 30_000 # number of steps
dt = 0.01 ; time step in ps
nstxout = 1000 ; number of steps to write checkpoint = nstxout
nstlog = 1000 ; number of steps to print log
nstcomm = 100 ; frequency for center of mass motion removal
; select HPS model, available options: hps_kr, hps_urry, or hps_ss
model = hps_urry
; control temperature coupling
tcoupl = yes
ref_t = 310 ; Kelvin- reference temperature
tau_t = 0.01 ; ps^-1
;pressure coupling
pcoupl = yes
ref_p = 1
frequency_p = 25
; Periodic boundary condition: if pcoupl is yes then pbc must be yes.
pbc = yes
; if pbc=yes, then use box_dimension option to specify box_dimension = x or [x, y, z], unit of nanometer
box_dimension = 30 ; [30, 30, 60]
; input
protein_code = FUS_100chains
pdb_file = FUS_100chains.pdb
; output
checkpoint = FUS_100chains.chk
;Use GPU/CPU
device = GPU
; If CPU is specified, then use ppn variable
ppn = 4
;Restart simulation
restart = no
minimize = yes ;if not restart, then minimize will be loaded, otherwise, minimize=False
General information
Simulation parameters are input from .ini file which is loaded by ConfigParser module in Python.
The section title [OPTIONS] is required, do not change section’s name.
Comment can be inline or in new line, start with ; or #
Keyword and value can be separated by = or :
Run control
md_steps: (long int)
(1) Maximum number of steps to integrate or minimize
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dt: (double)
(0.01)[ps] Time step for integration
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nstxout: (int)
(1) [step] number of steps that elapse between writing coordinates to output trajectory file,
the last coordinates are always written
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nstlog: (int)
(1) number of steps that elapse between writing energies to the log file
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nstcomm: (int)
(100) frequency for center of mass motion removal
Model parameter
There are three models supported now: hps_kr, hps_urry and hps_ss.
hps_kr has parameters for a wide range of residues, i.e RNA, phosphorylation residues … but this model is less accurate
model: (string)
hps_kr: Kapcha-Rossy hydropathy scale, parameterize from OPLS-AA forcefield
hps_urry (default): Urry hydropathy scale, parameterize from experiment
hps_ss: hps_urry with bonded potential (angle and torsion)
Temperature coupling
tcoupl: (bool)
yes (default) : The only available option for now, we don't care about NVE ensemble.
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ref_t: (double)
(300) [K] : Reference temperature in unit of Kelvin
------------------------------------------------------------------------------------
tau_t: (double)
[ps^-1] : The friction coefficient which couples the system to the heat bath (in inverse picoseconds)
Pressure coupling
pcoupl (bool)
yes : Using pressure coupling
no (default) : Run on NVT ensemble only
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ref_p (double)
(1) [bar] The default pressure acting on the system.
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frequency_p (int)
(25) [steps] the frequency at which Monte Carlo pressure changes should be attempted
Periodic boundary condition:
if pcoupl is yes then pbc must be yes.
pbc (bool)
yes : Using periodic boundary condition.
If this option is chosen, then it will affect to non-bonded forces in the system,
and the coordinate writen in PDB and DCD file as well. No worries since I have handled these.
no (default) : Without periodic boundary condition.
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box_dimension (float or list of float)
[nm] An example of box dimension:
If you want a cubic box of 30x30x30 nm^3, put: 30 or [30, 30, 30]
If you want a rectangular box? Put: [30, 30, 60]
File input/output
protein_code (string)
String for output prefix, i.e {protein_code}.dcd, {protein_code}.log
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pdb_file (string)
[.pdb, .cif] Input structure for loading topology and initial coordinate
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checkpoint (string)
[.chk] Checkpoint file name, here I ask you to provide it explicitly since
because checkpoint can be used to load state or save state.
in case if you restart simulation with different name, you have to provide it.
Simulation platform
Simulation can be run on CPU with number of threads is control by ppn or using GPU. If device=CPU then ppn need to be specify, otherwise simulation will run on 1 core
device (string)
GPU : Use gpu to run simulation
CPU (default) : use cpu to run simulation, if you specify cpu, you should modify ppn option, it control
how many cores will be used to run simulation, if not, default is 1.
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ppn (int)
(1) [threads] Number of threads used to run simulation on CPU. When using GPU,
performance is boosted a lot so ppn in that case is set to 1.
Restart simulation
restart (bool)
yes : restart simulation from checkpoint file. This can be True, 1 or whatever are not (FALSE)
in python condition. If this option is selected, minimize will be force to False.
no (default) : Run simulation from beginning, if this option is selected, you can choose if you want to minimize your
system before running simulation.
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minimize (bool)
yes (default) : perform energy minimization before run molecular dynamics.
no : Not running energy minimization. This is default option when restart option is set to yes.