[gmx-users] gmx v3.1 vs v3.2
Derrick Guang Yuh Lee
k24dgyl at mun.ca
Mon May 2 03:32:10 CEST 2005
David,
The Warnings are the same for both, one about the positive charge involved
in POPC and one about:
--------------------------------------------------------
WARNING 2 [file "popc.top", line 19]:
7380 non-matching atom names
atom names from popc.top will be used
atom names from popc128a.gro will be ingnored
--------------------------------------------------------
and the differences between the two files, using gmxcheck, were:
--------------------------------------------------------
nstcheckpoint (0 - 1000)
andersen_seed (0 - 815131)
nstgbradii (0 - 1)
rgbradii (0 - 2)
dihre_fc (0 - 1000)
nstdihreout (0 - 100)
and some differences between their idef.
Any insight? Thanks for your help.
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 Sat, 30 Apr 2005, David wrote:
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> 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.
>
More information about the gromacs.org_gmx-users
mailing list