[gmx-users] gmx v3.1 vs v3.2

[David]

On Fri, 2005-04-29 at 19:45 -0230, Derrick Guang Yuh Lee wrote:
> Dear David and anyone else,
> 
> It is a problem with the acutal input files; that is, the mdp, gro, and
> top files. For example, when I did some simulations on v3.1.4 using Dr.
> Tieleman's POPC bilayer, it worked fine, but w/ those same input files
> on v3.2, I either got segmentation faults or "Warning 1-4 interaction...".
> It seems like it should be a problem w/ the mdp parameters, so I checked
> the gmx-user archive and used an example mdp file:
> 
> http://www.gromacs.org/pipermail/gmx-users/2003-February/004363.html
> 
> but I got the same results. v3.2 gave me "Warning 1-4 interaction..."
> and just stalls there, but with v3.1.4, it does produce something. Also,
> when I switch the parameter value for coulombtype to Cut-off instead of
> PME, in both my original files and the example mdp file, it does produce
> the appropriate output files. So I guess that causes another question to
> arise, which is more appropriate PME or Cut-off for lipid simulations?
> Thanks in advance.
> 
Cut-off is never appropriate...

Did you carefully check grompp warnings, I seem to remember there was an
issue with parameter files being included multiple times. Do also run
this:
gmxcheck -s1 top314.tpr -s2 top321.tpr | less
and see where the differences are.


> 
> 
> Sincerely
> 
>  - Derrick Lee
> 
> 
>  Derrick Guang Yuh Lee
>  Department of Mathematics and Statistics / Department of Biochemistry
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca / derrickglee at hotmail.com
> 
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst."
>                                                               - bruce lee
> 
> On Tue, 26 Apr 2005, David wrote:
> 
> > On Tue, 2005-04-26 at 15:51 -0230, Derrick Guang Yuh Lee wrote:
> > > Dear Gmx-Users,
> > >
> > > I was curious if anyone would be able to explain a little problem I am
> > > having between two versions of GROMACS; on one computer I am running v3.14
> > > and on the other one, I am running v3.2. So,  when I run, for example, an
> > > energy minimzation of a particular lipid simulation on the computer with
> > > v3.14, it works fine, but when I run the exact same files on the computer
> > > w/ v3.2, i get:
> > can you be more specific? Is this the same tpr file, or the same input
> > files for grompp? In the latter case I would advise you to compare the
> > tpr files from 314 to 321 using gmxcheck.
> >
> > >
> > > -------------------------------------------------------------
> > > Steepest Descents:
> > >    Tolerance (Fmax)   =  	value
> > >    Number of steps    =         value
> > > Segmentation fault
> > > -------------------------------------------------------------
> > >
> > > If anyone can clear this one up it would be most appreciated. Thanks.
> > >
> > >
> > >
> > > Sincerely
> > >
> > >  - Derrick Lee
> > >
> > >
> > >  Derrick Guang Yuh Lee
> > >  Department of Mathematics and Statistics / Department of Biochemistry
> > >  Memorial University of Newfoundland
> > >  k24dgyl at mun.ca / derrickglee at hotmail.com
> > >
> > > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > > truth that each student must find for himself. a good teacher is merely a
> > > catalyst."
> > >                                                               - bruce lee
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > 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 gmx-users-request at gromacs.org.
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> >
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++