[gmx-users] job magic number in MXMPI_MAGIC
omovie_johnnie at hotmail.com
Sat Aug 18 01:34:24 CEST 2007
I have tried that in the past though, and I still get Epot values of nan.
It seems the only other option I have is to place the molecules in separate boxes, set
disre=simple, and use the -multi option during the mdrun. The -multi option only works with the parallel installation.
Unfortunately I get the ff error message when I try to use the parallel gromacs installation on the server:
<MPICH-MX> Error: Need to obtain the job magic number in MXMPI_MAGIC.
I would appreciate any advice on how to fix this.
> Date: Fri, 17 Aug 2007 20:46:58 +0100> From: t.piggot at bristol.ac.uk> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] Step size too small> > Hi,> > I do not think that what Per suggests is the problem, if you look at the > potential energy after the minimisation this value is huge (and the other > two values are inf!). The problem is most likely with your topology. As you > say the two molecules have been successfully minimised on their own so I > would suggest that your problem is with either how you edit the .top file > or the distance restraint between the molecules. For my protein that has > more than one identical chains pdb2gmx does not recognise them as one if > you provide different chain identifiers in the pdb file, so doing this > should hopefully stop you having to edit the .top file.> > Hope this helps> > Tom> > --On 17 August 2007 19:02 +0200 Per Larsson <per.larsson at sbc.su.se> wrote:> > > Hello!> >> >> > Check out> > http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan> > ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_> > precision> >> >> > Cheers> > /Per> >> >> >> > 17 aug 2007 kl. 18.28 skrev Sheyore Omovie:> >> > Dear gmx-users,> > > > I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited> > the .top file to remove the bonds created between the two molecules, I> > also added a distance restraint btw the molecules. (The 2 structures have> > been separately minimized). However, I get the ff message for EM run:> >> > Stepsize too small, or no change in energy.> > Converged to machine precision,> > but not to the requested precision Fmax < 1000> > > > Double precision normally gives you higher accuracy.> > > > Steepest Descents converged to machine precision in 15 steps,> > but did not reach the requested Fmax < 1000.> > Potential Energy = 1.0246325e+20> > Maximum force = inf on atom 1> > Norm of force = inf I would appreciate any advice on how> > to fix this.> > Rgds> > John> >> >> > __________________________________________________> > See what you’re getting into?before you go there See it!> > _______________________________________________> > gmx-users mailing list gmx-users at gromacs.org> > 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 gmx-users-request at gromacs.org.> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php> >> >> > > > ----------------------> TJ Piggot> t.piggot at bristol.ac.uk> University of Bristol, UK.> > _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> 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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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