Well, no. I got a 20GB log file when nstlog was 1000. When I changed it to 10000, the log file was about 1 MB after a few minutes of simulation which means that it will be in GBs in a few days.
On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel <gauravgoel...@gmail.com>wrote: > You've set the frequency of writing to log file as > 'nstlog = 100000'. > Given that 'nsteps = 100000000', you're writing to the > log file only 1000 times. Do you get a 20GB md.log file with these settings? > > -Gaurav > > On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain < > nimeshjain2...@u.northwestern.edu> wrote: > >> Hi, >> >> I am having some problem in my simulations related to log files. The file >> sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log >> file. One of my grompps looks like this: >> [tau_t is very low because I am using bd and it doesn't work otherwise]. >> [I am doing a replica exchange with 10,000 as exchange frequency] >> >> >> 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 >> >> nstlog = 100000 >> nstenergy = 1000 >> >> nstxtcout = 1000 >> xtc-precision = 1000 >> >> 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 P260 SA SB >> >> energygrp_table = A A A T A G A C A P260 A SA A SB T T T >> G T C T P260 T S >> A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB P260 P260 >> P260 SA P260 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 = 0.0001 >> ref_t = 260.00 >> >> Pcoupl = No >> >> andersen_seed = 815131 >> >> gen_vel = yes >> gen_temp = 260.0000 >> gen_seed = 1993 >> >> ; ENERGY GROUP EXCLUSIONS >> ; Pairs of energy groups for which all non-bonded interactions are >> excluded >> energygrp_excl = >> >> >> >> Please let me know if anyone knows whats the problem. >> >> Thanks, >> Nimesh >> >> -- >> 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/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/mailing_lists/users.php >> > > > -- > 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/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/mailing_lists/users.php > -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern University
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