Hi Berk, Thanks for the update.
I think steepest descent will be enough for me indeed. But I was not really sure about the preferred value for emtol ... I was using 1.0 following a colleague! Thanks again. Regards, Suman. On Sat, Nov 22, 2008 at 1:58 AM, Berk Hess <[EMAIL PROTECTED]> wrote: > Hi, > > I fixed the bug for version 4.0.3. > There was also a bug with writing the forces at the end > with nstfout=0. > > But if you are minimizing for starting a md simulation, > you do not need cg, steepest descents is enough > (with em_tol of 1000 or 100). > > Note that in 4.0 you can now minimize with constraints, > box for water and other molecules. > > If you really need to run parallel cg now, you can use > the -pd switch of mdrun. > > Berk > > > >> Date: Sat, 22 Nov 2008 00:37:18 +0530 >> From: [EMAIL PROTECTED] >> To: [email protected] >> Subject: [gmx-users] Gromacs-4.0.2: energy minimization error in parallel >> version >> >> Dear all, >> >> I am trying to use mdrun_mpi for energy minimization over 2/4/8 nodes. >> But in every case the run gets aborted with the following error: >> >> ------------------------------------------------------- >> Program mdrun_mpi, VERSION 4.0.2 >> Source code file: minimize.c, line: 404 >> >> Software inconsistency error: >> state mismatch in do_em_step >> ------------------------------------------------------- >> >> What could be the reason behind this? As far as I remember I have not >> faced this problem in 3.3.3 version. Not that I regularly use parallel >> version for energy minimization, but it would be nice to be able to >> sort out this problem. The PR or MD run goes fine in the same >> settings. >> >> The mdp file is: >> >> title = cg+steep energymin spce watbox >> cpp = /lib/cpp >> define = -DFLEXIBLE >> >> integrator = cg >> nsteps = 5000 >> nstcgsteep = 1000 >> comm_mode = linear >> nstcomm = 1 >> >> emtol = 1.0 >> emstep = 0.01 >> >> nstxout = 100 >> nstvout = 100 >> nstfout = 100 >> nstlog = 100 >> nstenergy = 100 >> energygrps = protein sol >> >> nstlist = 5 >> ns_type = grid >> pbc = xyz >> rlist = 0.9 >> >> coulombtype = PME >> rcoulomb = 0.9 >> >> vdwtype = cut-off >> rvdw = 1.2 >> >> fourier_spacing = 0.12 >> pme_order = 6 >> ewald_rtol = 1e-6 >> optimize_fft = yes >> >> constraints = none >> >> >> >> Thanks, >> Suman. _______________________________________________ gmx-users mailing list [email protected] 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
