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Hi,<br><br>I fixed the bug for version 4.0.3.<br>There was also a bug with writing the forces at the end<br>with nstfout=0.<br><br>But if you are minimizing for starting a md simulation,<br>you do not need cg, steepest descents is enough<br>(with em_tol of 1000 or 100).<br><br>Note that in 4.0 you can now minimize with constraints,<br>box for water and other molecules.<br><br>If you really need to run parallel cg now, you can use<br>the -pd switch of mdrun.<br><br>Berk<br><br><br><br>> Date: Sat, 22 Nov 2008 00:37:18 +0530<br>> From: suman@sscu.iisc.ernet.in<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Gromacs-4.0.2: energy minimization error in parallel version<br>> <br>> Dear all,<br>> <br>> I am trying to use mdrun_mpi for energy minimization over 2/4/8 nodes.<br>> But in every case the run gets aborted with the following error:<br>> <br>> -------------------------------------------------------<br>> Program mdrun_mpi, VERSION 4.0.2<br>> Source code file: minimize.c, line: 404<br>> <br>> Software inconsistency error:<br>> state mismatch in do_em_step<br>> -------------------------------------------------------<br>> <br>> What could be the reason behind this? As far as I remember I have not<br>> faced this problem in 3.3.3 version. Not that I regularly use parallel<br>> version for energy minimization, but it would be nice to be able to<br>> sort out this problem. The PR or MD run goes fine in the same<br>> settings.<br>> <br>> The mdp file is:<br>> <br>> title = cg+steep energymin spce watbox<br>> cpp = /lib/cpp<br>> define = -DFLEXIBLE<br>> <br>> integrator = cg<br>> nsteps = 5000<br>> nstcgsteep = 1000<br>> comm_mode = linear<br>> nstcomm = 1<br>> <br>> emtol = 1.0<br>> emstep = 0.01<br>> <br>> nstxout = 100<br>> nstvout = 100<br>> nstfout = 100<br>> nstlog = 100<br>> nstenergy = 100<br>> energygrps = protein sol<br>> <br>> nstlist = 5<br>> ns_type = grid<br>> pbc = xyz<br>> rlist = 0.9<br>> <br>> coulombtype = PME<br>> rcoulomb = 0.9<br>> <br>> vdwtype = cut-off<br>> rvdw = 1.2<br>> <br>> fourier_spacing = 0.12<br>> pme_order = 6<br>> ewald_rtol = 1e-6<br>> optimize_fft = yes<br>> <br>> constraints = none<br>> <br>> <br>> <br>> Thanks,<br>> Suman.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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