Sorry, I forgot to mention that one cofactor NDP, I added in my molecule using PRODRG server.
2008/9/12 vivek sharma <[EMAIL PROTECTED]> > Hi Carsten, > Thanks for your reply. Actually I am running MD simulation on a protein > molecule with 270 residues(2687 atoms), after adding water it is having > 45599 atoms, and using the recent version of gromacs test available from > gromacs.org (gmxtest-3.3.3.tgz) > Following are the entries from the .mdp file I am using..... > > **********md.mdp > title = trp_drg MD > cpp = /lib/cpp ; location of cpp on SGI > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 25000 ; total 50 ps. > nstcomm = 1 > nstxout = 2500 ; output coordinates every 5.0 ps > nstvout = 0 > nstfout = 0 > nstlist = 5 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 6 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Berendsen temperature coupling is on in four groups > Tcoupl = berendsen > tau_t = 0.1 0.1 0.1 > tc-grps = protein NDP sol > ref_t = 300 300 300 > ; Pressure coupling is on > Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > > > ****************and Following are the commands I am using > grompp_d -np 128 -f md1.mdp -c 1XU9_A_b4em.gro -p 1XU9_A.top -o > 1XU9_A_md1_np128.tpr > > submit > mdrun_d > /////arguement for mdrun_d > -s 1XU9_A_md1_np128.tpr -o 1XU9_A_md1_np128.trr -c 1XU9_A_pmd1_np128.gro -g > md_np128.log -e md_np128.edr -np 128 > > ***********Following is the error I am getting > Reading file 1XU9_A_md1_np128.tpr, VERSION 3.3.3 (double precision) > starting mdrun 'CORTICOSTEROID 11-BETA-DEHYDROGENASE, ISOZYME 1' > 25000 steps, 50.0 ps. > > srun: error: n141: task1: Segmentation fault > srun: Terminating job > > **************************************************************** > Is this information is helpfull in figuring out the problem. > Please, advice > > With Thanks, > Vivek > > 2008/9/11 Carsten Kutzner <[EMAIL PROTECTED]> > > vivek sharma wrote: >> >>> Hi There, >>> I am running gromacs parellal version on cluster, with different -np >>> options. >>> >> Hi, >> >> which version of gromacs exactly are you using? > > > > >> >> >> On analyzing the 5 nsec trajectory using ngmx, I am finding difference in >>> the trajectory of two similar runs (only thing varying in two runs in -np >>> i.e 20 and 64 ), where mdp file and input files are same in two cases. >>> I am wondering why I am getting this difference in two trajectories ? >>> I am looking for the advice whether I did something wrong or what may be >>> the probable reason for this difference. >>> >> >> There are many reasons why a parallel run does not yield binary identical >> results to a run with another number of processors, even if you start from >> the same tpr file. If you use PME, then the FFTW could pick a slightly >> different algorithm (it will select the fastest for that number of >> processors. >> This feature you can turn off by passing --disable-fftw-measure to the >> gromacs configure script). But still you can get results that are not >> binary identical if you do FFTs on a varying number of CPUs. Also, for >> limited accuracy which is inherent to any computer, additions need not >> be associative, which can show up in parallel additions. >> >> Generally, if you run in double precision, these effects will be way >> smaller, >> but nevertheless you won't get binary identical results. This will in all >> cases lead to trajectories which slowly diverge from each other. However, >> in the fist few hundred time steps, you should not see any difference in >> the first couple of decimals of the variables (positions, velocities, >> energies ...) >> >> Also, I am not able to run gromacs faster by increasing the -np issue, >>> >> >> Please provide the exact command line you used. >> >> Is there any max limit for scaling gromacs on parellal cluster ? >>> >> >> Yes, depending on your MD system and on the cluster you use :) >> >> Carsten >> >> >> With Thanks, >>> Vivek >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.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 >>> >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics Department >> Am Fassberg 11 >> 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www.mpibpc.mpg.de/research/dep/grubmueller/ >> http://www.gwdg.de/~ckutzne <http://www.gwdg.de/%7Eckutzne> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.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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