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