Hi, all, I was able to fix the problem by:
1) Reducing my PME order from 6 to 4 2) Reducing my Fourier spacing from 0.12 to 0.06 3) Also, I had to do comm_grps = System or comm_grps = Protein Best wishes, Art --- Dongsheng Zhang <[EMAIL PROTECTED]> wrote: > Dear Erik, > > I had the same problem as Arthur Roberts. So I > downloaded your new > version of gmx_system_xdr.h and gmx_system_xdr.c > from > http://bugzilla.gromacs.org/show_bug.cgi?id=55 > > Before I recompile gromacs, I checked the difference > between your new > version and the old one. The result is as follows: > > diff gmx_system_xdr.c gmx_system_xdr-n.c > 2c2 > < * $Id: gmx_system_xdr.c,v 1.5.4.1 2006/03/09 > 08:12:16 lindahl Exp $ > --- > > * $Id: gmx_system_xdr.c,v 1.5 2004/01/23 17:23:13 > lindahl Exp $ > > diff gmx_system_xdr.h gmx_system_xdr-n.h > 2c2 > < * $Id: gmx_system_xdr.h,v 1.3.4.1 2006/03/09 > 08:12:09 lindahl Exp $ > --- > > * $Id: gmx_system_xdr.h,v 1.3 2003/11/17 21:50:40 > spoel Exp $ > > Both differences are in documentation. I am confused > how your > modification can solve the problem. > > I had the same problem and posted in the mailing > list before ( > http://www.gromacs.org/pipermail/gmx-users/2006-June/022493.html > ) I > also found Jason O'Young had asked the similar > question at > http://www.gromacs.org/pipermail/gmx-users/2006-May/021605.html > > I think this problem sounds common, could you please > investigate what's > wrong? Thank you very much for your help! > > By the way, I can continue the simulation by > tpbconv, but hangs soon > without any error message. The "top" command shows > the programs is > running, but no more output data. > > > All the best! > > Dongsheng > > > On Mon, 2006-07-31 at 08:36 +0200, Erik Lindahl > wrote: > > Hi, > > > > It _might_ be solved by the fix attachment at > > > > http://bugzilla.gromacs.org/show_bug.cgi?id=55 > > > > (also in CVS) > > > > Cheers, > > > > Erik > > > > On Jul 31, 2006, at 8:11 AM, Arthur Roberts wrote: > > > > > Hi, all, > > > > > > I am trying to run Gromacs on a P655+ with Aix > 5.2. > > > Initially, mdrun appears to work, but always > hangs. > > > Eventually, I get timed out from the > supercomputer > > > with no data to show for it. Below is a link > > > detailing the problem: > > > > > > > http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hangs- > > > > without-showing-steps.html > > > > > > I appreciate your input. Your previous > suggestions > > > have been very helpful. > > > > > > Best wishes, > > > Art > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > 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 > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > 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 > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
