[gmx-users] Issue running gromacs in Cluster

[Broadbent, Richard]

On 13/05/2013 08:46, "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

This writes out every 0.4 ps I doubt that¹s what you want

>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?*

No you are writing every 200 steps not ps this is explained in the
turtorials and the manual
You can check the file size by looking at ls -lh my guess is both the trr
and xtc will be gigantic

>*
>*
>*Please help*
>*
>*
>*Thanks,*
>*Nitin*
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