about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy of my mdp file.
title = BMIM+PF6 cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 20000000 ; total 4ns. nstcomm = 1 nstxout = 50000 nstvout = 50000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = Shift rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.6 ;pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc_grps = BMI PF6 tau_t = 0.1 0.1 ref_t = 300 300 nsttcouple = 1 ; Energy monitoring energygrps = BMI PF6 ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps = BMI PFF tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 100000 On Thu, Jan 27, 2011 at 4:12 PM, Dallas Warren <dallas.war...@monash.edu>wrote: > You will need to provide more details on the system. How many atoms, what > sort of computer system is it being run on, how many nodes, copy of the mdp > file etc. > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Denny Frost > *Sent:* Friday, 28 January 2011 9:34 AM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-users] Slow Runs > > > > I am taking over a project for a graduate student who did MD using Gromacs > 3.3.3. I now run similar simulations with Gromacs 4.5.1 and find that they > run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs > 3.3.3. The runs have about the same number of atoms and both use opls force > fields. The mdp files is virtually the same (I copied them). The only > major difference is that my runs have difference species and thus have > different (although smaller) itp files. The runs are stable and give > reasonable thermodynamic properties - they're just slow. Has anyone had any > experience with something like this? > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >
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