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* -- 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