Thanks Tom,
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.
Rgds
John
> Date: Fri, 17 Aug 2007 20:46:58 +0100> From: [EMAIL PROTECTED]> To:
> [email protected]> 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 <[EMAIL PROTECTED]>
> 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
> [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> >> >> > > >
> ----------------------> TJ Piggot> [EMAIL PROTECTED]> University of Bristol,
> UK.> > _______________________________________________> 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
_________________________________________________________________
Recharge--play some free games. Win cool prizes too!
http://club.live.com/home.aspx?icid=CLUB_wlmailtextlink
_______________________________________________
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
