GROMACS version: 2021
GROMACS modification: Yes
Hello, I am using the below .mdp file to apply acceleration to the methane molecules (residue name _U1M) in the X-direction.
When I run the gmx energy command, I get Ux_U1M, Uy_U1M, and Uz_U1M as output options. However, they all have 0 values.
So, How can I know if the code is applying the required acceleration or not? and how can I quantify the pressure gradient across the X-direction due to this acceleration?
title = NVT non-equilibrium simulation with acceleration
;define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 0.001 * 250000 = 250 ps
dt = 0.001 ; 1 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 0.95 ; short-range electrostatic cutoff (in nm)
rvdw = 0.95 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = system ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 330 ; 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
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 330 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; coordinate coupling
refcoord-scaling = com
; Acceleration for external force application
acc-grps = _U1M
accelerate = 1 0 0