If you can rule out file permissions issues (because you wrote files earlier), and actually running out of disk, usually that would suggest a flaky network file system.
Mark On Mon, Apr 21, 2014 at 4:09 PM, Andrew Bostick <andrew.bosti...@gmail.com>wrote: > 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. > -- 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.