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.broadben...@imperial.ac.uk> wrote: > > > On 13/05/2013 08:46, "Sainitin Donakonda" <saigr...@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* > >-- > >gmx-users mailing list gmx-users@gromacs.org > >http://lists.gromacs.org/mailman/listinfo/gmx-users > >* Please search the archive at > >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >* Please don't post (un)subscribe requests to the list. Use the > >www interface or send it to gmx-users-requ...@gromacs.org. > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
