One more point: when I run the job interactively, although it works but date and time are wrong!
step 0 step 100, will finish Wed Sep 16 16:16:00 2009 step 200, will finish Wed Sep 16 14:32:34 2009 step 300, will finish Wed Sep 16 13:57:51 2009 step 400, will finish Wed Sep 16 11:35:46 2009 step 500, will finish Wed Sep 16 11:50:12 2009 step 600, will finish Wed Sep 16 10:36:38 2009 step 700, will finish Wed Sep 16 09:44:04 2009 step 800, will finish Wed Sep 16 10:07:02 2009 step 900, will finish Wed Sep 16 09:29:25 2009 step 1000, will finish Wed Sep 16 08:59:19 2009 step 1100, will finish Wed Sep 16 09:20:06 2009 step 1200, will finish Wed Sep 16 08:55:47 2009 step 1300, will finish Wed Sep 16 09:13:38 2009 step 1400, will finish Wed Sep 16 08:53:15 2009 Is it a cluster related or GROMACS related issue? Is it important at all? Payman On Wed, 2009-08-26 at 22:06 -0600, Paymon Pirzadeh wrote: > I made a .tpr file for my md run without any problems (using the bottom > mdp file). My job submission script is also the same thing I used for > other jobs which had no problems. But now when I submit this .tpr file, > only an empty log file is generated! The qstat of the cluster shows that > the job is running, also the processors are 100% engaged while I have no > outputs! > Here is my mdp file: > title = Yo > cpp = cpp > include = -I../top > define = -DPOSRES > > ; Run control > > integrator = md > dt = 0.001 ;1 fs > nsteps = 3000000 ;3 ns > comm_mode = linear > nstcomm = 1 > > ;Output control > > nstxout = 5000 > nstlog = 5000 > nstenergy = 5000 > nstxtcout = 1500 > nstvout = 5000 > nstfout = 5000 > xtc_grps = > energygrps = > > ; Neighbour Searching > > nstlist = 10 > ns_type = grid > rlist = 0.9 > pbc = xyz > > ; Electrostatistics > > coulombtype = PME > rcoulomb = 0.9 > ;epsilon_r = 1 > > ; Vdw > > vdwtype = cut-off > rvdw = 1.2 > DispCorr = EnerPres > > ;Ewald > > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-6 > optimize_fft = yes > > ; Temperature coupling > > tcoupl = v-rescale > ld_seed = -1 > tc-grps = System > tau_t = 0.1 > ref_t = 275 > > ; Pressure Coupling > > Pcoupl = no > ;Pcoupltype = isotropic > ;tau_p = 1.0 > ;compressibility = 5.5e-5 > ;ref_p = 1.0 > gen_vel = yes > gen_temp = 275 > gen_seed = 173529 > constraint-algorithm = Lincs > constraints = all-bonds > lincs-order = 4 > > I am not sure where things go wrong! > > Payman > > > > > > > > > > > > > On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: > > Paymon Pirzadeh wrote: > > > Can I change the charge of Na ion added from +1 to +0.99 to cancel the > > > negative charge exactly? Does that hurt science or simulation? > > > > It's probably irrelevant. The representation of "decimal" numbers on > > computers can be inexact, such that things like 0.02 added to itself 100 > > times does not pass a test for equality with 2. You may be observing > > this kind of thing here. Your protein's [atoms] directive has a running > > count of the total charge on the molecule - go and read it and see that > > each residue has an integral charge. Hopefully you can observe where the > > rounding error might be occurring and you can make a judgement about > > whether this might be true. > > > > Mark > > _______________________________________________ > > 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 > > _______________________________________________ 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
