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