- constant-temperature and -volume equilibration of a system
macros.xml
> verbose.txt &&
gmx mdrun -deffnm nvt &>> verbose.txt
#if $str == 'pdb' or $str == 'both'
&& gmx editconf -f nvt.gro -o nvt.pdb &>> verbose.txt
#end if
]]>
#if $mdp.mdpfile == 'default':
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = $mdp.integrator ; leap-frog integrator
nsteps = $mdp.md_steps ; 2 * 50000 = 100 ps
dt = $mdp.step_length ; 2 fs
; Output control
nstxout = $mdp.write_freq ; save coordinates every n ps
nstvout = $mdp.write_freq ; save velocities every n ps
nstenergy = $mdp.write_freq ; save energies every n ps
nstlog = $mdp.write_freq ; update log file every n ps
nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = $mdp.cutoffscheme
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off
rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list.
rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off
; Electrostatics
coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
#end if
str == 'gro' or str == 'both'
str == 'pdb' or str == 'both'
traj == 'trr' or traj == 'both'
traj == 'xtc' or traj == 'both'
capture_log