[gmx-users] Issue running gromacs in Cluster

[XAvier Periole]

You may have created large files and thus got out of quota on the disc. 

Check your quota and consider reducing the frequency of saving coordinates. 

On May 13, 2013, at 9:46, Sainitin Donakonda <saigro16 at gmail.com> wrote:

> 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*
> -- 
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