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

[Derrick Guang Yuh Lee]

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.



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
> >
> > _______________________________________________
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> --
> 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
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