[gmx-users] Cannot Generate .gro and .cpt files after running nvt

[Chenyu Liu]

Sorry about the format issue in the previous email. I hope this will give
you a better view for the mdp file I use to run nvt simulations.
title                   = CHARMM PKA NVT equilibration

define                  = -DPOSRES  ; position restrain the protein

; Run parameters

integrator              = md        ; leap-frog integrator

nsteps                  = 5000000   ; 2 * 5000000 = 10 ns

dt                      = 0.002     ; 2 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    = shake     ; Shake Algorithm is Applied

constraints             = h-bonds   ; bonds involving H are constrained

; Nonbonded settings

cutoff-scheme           = Verlet    ; Buffered neighbor searching

ns_type                 = grid      ; search neighboring grid cells

nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet

rcoulomb                = 1.0       ; short-range electrostatic cutoff (in
nm)

rvdw                    = 1.0       ; 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                 = Protein Non-Protein   ; two coupling groups -
more accurate

tau_t                   = 0.1     0.1           ; time constant, in ps

ref_t                   = 300     300           ; 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 sch

; Velocity generation

gen_vel                 = yes       ; assign velocities from Maxwell
distribution

gen_temp                = 300       ; temperature for Maxwell distribution

gen_seed                = -1        ; generate a random seed