I set nstlog = 100000000000, and still I get a 5MB log file within a minute of starting the sim. It seems absurd, but its happening :(
On Thu, Dec 16, 2010 at 10:05 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Nimesh Jain wrote: > >> Hi, >> >> I am trying to simulate a system of 880 particles with implicit solvent >> using brownian dynamics, but the simulation generates huge log files (it >> writes md.log files at a rate of almost 5MB/minute) and this crashed my >> system since I ran out of space :( >> >> My mdp file looks like this: >> >> include = >> define = >> integrator = bd >> tinit = 0 >> dt = 0.001 >> nsteps = 100000000 ;100000 >> simulation_part = 1 >> init_step = 0 >> comm-mode = Angular >> nstcomm = 1 >> comm-grps = >> >> emtol = 0.01 >> emstep = 1.5 >> >> nstxout = 10000 >> nstvout = 10000 >> nstfout = 10000 >> >> nstenergy = 1000 >> >> nstxtcout = 1000 >> xtc-precision = 1000 >> >> nstlog = 0 >> >> xtc-grps = >> energygrps = >> >> ns_type = grid >> pbc = xyz >> periodic_molecules = no >> >> rlist = 8.95 >> >> coulombtype = user >> rcoulomb-switch = 0 >> rcoulomb = 8.95 >> epsilon-r = 1 >> >> vdw-type = user ;cutoff >> rvdw-switch = 0 >> rvdw = 8.95 >> DispCorr = No >> table-extension = 1 >> >> ; Seperate tables between energy group pairs >> energygrps = A T G C P300 SA SB >> >> >> energygrp_table = A A A T A G A C A P300 A SA A SB T T T >> G T C T P300 T SA T SB G G G C G P300 G SA G SB C C C P300 C SA >> C SB P300 P300 P >> 300 SA P300 SB SA SA SA SB SB SB >> >> ; Spacing for the PME/PPPM FFT grid >> fourierspacing = 0.10 >> >> Tcoupl = Nose-Hoover >> tc-grps = System >> tau_t = 0.001 >> > > This doesn't seem like a reasonable setting for tau_t; grompp should have > warned you about that since dt = tau_t! > > > ref_t = 300.00 >> >> Pcoupl = No >> >> andersen_seed = 815131 >> >> gen_vel = yes >> gen_temp = 300.0000 >> gen_seed = 1993 >> >> Please let me know if there is a solution to write smaller mdp files. I >> have set nstlog = 0 , but even that doesn't work! >> > > Set nstlog to some incredibly large number, then, and it will only output a > few times. It seems strange that nstlog = 0 didn't suppress the .log file > output as it would any of the other nst* settings. > > -Justin > > >> Thanks >> Nimesh >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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