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