Dear gromacs users I am doing md simulation on the a protein with 190 residues.
I did minimization and equilibration without problem and error. But in production run step (last md simulation with 15000000 steps), in step 6500000, I encountered with following error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. my mdp file is as follows: ----------------------------------------------------------------------------------------- title = opls Protein MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 15000000 ; 0.002 * 500000 = 1000 ps, 30 ns dt = 0.002 ; 2 fs ; Output control nstxout = 3000 ; save coordinates every 2 ps nstvout = 3000 ; save velocities every 2 ps nstxtcout = 3000 ; xtc compressed trajectory output every 2 ps nstenergy = 3000 ; save energies every 2 ps nstlog = 3000 ; update log file every 2 ps energygrps = Protein Ion ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off ----------------------------------------------------------------------------------------- If I use df -h command to know disk space, I obtained following information: Filesystem Size Used Avail Use% Mounted on /dev/sda3 220G 14G 196G 7% / none 4.0K 0 4.0K 0% /sys/fs/cgroup udev 3.0G 4.0K 3.0G 1% /dev tmpfs 607M 1.3M 606M 1% /run none 5.0M 0 5.0M 0% /run/lock none 3.0G 152K 3.0G 1% /run/shm none 100M 64K 100M 1% /run/user /dev/sda6 245G 61G 184G 25% /media/pdfco/my dear /dev/sda2 220G 85G 136G 39% /media/pdfco/Windows /dev/sda5 245G 43G 202G 18% /media/pdfco/nazif ------------------------------------------------------------------------------------------ Is my computer system suitable for this md simulation? How to solve this error? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.