[gmx-users] Issue running gromacs in Cluster
Sainitin Donakonda
saigro16 at gmail.com
Mon May 13 10:44:50 CEST 2013
Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..
*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the solution for this error ? is this same problem with saving 200
steps? or some thing else
Thanks,
Sainitin
On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard <
richard.broadbent09 at imperial.ac.uk> wrote:
>
>
> 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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