[gmx-users] Issue running gromacs in Cluster

[Sainitin Donakonda]

Hello,

I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file

; 7.3.3 Run Control
integrator              = md                    ; leap-frog integrator
dt                      = 0.002                 ; 2 fs
nsteps                  = 5000000                ; maximum number of steps
to integrate



; 7.3.8 Output Control
nstxout     = 200         ; suppress .trr output
nstvout     = 200        ; suppress .trr output
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 1000      ; write .xtc trajectory every 2 ps
energygrps  = Protein LIG

; 7.3.9 Neighbor Searching
nstlist                 = 5             ; [steps] freq to update neighbor
list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 1.2           ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 1.2           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = switch       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 1.2           ; [nm] distance for LJ cut-off
rvdw_switch             = 0.8           ; Start switching th LJ potential
DispCorr                = EnerPres         ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing          = 0.12          ; [nm] grid spacing for FFT grid
when using PME
pme_order               = 4             ; interpolation order for PME, 4 =
cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl                  = V-rescale                     ; temperature
coupling with Berendsen-thermostat
tc_grps                 = Protein_LIG Water_and_ions    ; groups to couple
seperately to temperature bath
tau_t                   = 0.1        0.1                ; [ps] time
constant for coupling
ref_t                   = 300        300                ; [K] reference
temperature for coupling

; Pressure coupling
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, bar^-1
refcoord_scaling    = com

; 7.3.17 Velocity Generation
gen_vel                 = no            ; velocity generation turned off

; 7.3.18 Bonds
constraints             = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
continuation            = yes           ; apply constraints to the start
configuration
lincs_order             = 4             ; highest order in the expansion of
the contraint coupling matrix
lincs_iter              = 1             ; number of iterations to correct
for rotational lengthening
lincs_warnangle         = 30            ; [degrees] maximum angle that a
bond can rotate before LINCS will complain


*and im using following commands dividing 20 ns to 10 ns each via extending
simulation*


*#This is the first simulation MD.mdp file contains 20 ns setup*
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

*#This extends 10 ns simulation*
tpbconv -s MD_first10.tpr -extend 10000 -o md_extended.tpr

mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16


But it is crashed giving following error

*XTC error - maybe you are out of quota?*
*
*
*dont know why it happened it is because as im saving .trr file every
200ps? is it creating large files? or should i give different name in
extending simulation?*
*
*
*Please help*
*
*
*Thanks,*
*Nitin*