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
