On Wed, Aug 11, 2010 at 1:10 PM, Nimesh Jain < [email protected]> wrote:
> 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. > > Did you re-compile using grompp after changing nstlog? Otherwise in md.tpr (output of grompp), nstlog=1000. -Gaurav > > On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel <[email protected]>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 < >> [email protected]> 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 [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Nimesh Jain > Graduate Student > Biomedical Engineering > Northwestern University > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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