[gmx-users] very strange directory dependent segmentation faults please HELP!

[Daan van Aalten]

Dear Semen

As a start for your topology you could put it into the PRODRG server at
http://davapc1.bioch.dundee.ac.uk/prodrg

Daan

On Fri, 26 Dec 2003, Semen Esilevsky wrote:

> Dear gmx users!
> Happy holidays to all!
> My question was probably discussed many times, but
> anyway.
> I have a custom molecule (flavone derivative) which
> has to be simulated in the lipid membrane. I have pdb
> coordinates for flavone, but there are no force field
> parameters for it. Is it enough to simulate it, or I
> have to construct forcefield? If yes how?
>
> Semen
>
> --- Lieven Buts <lieven at ultr.vub.ac.be> wrote:
> > On Wednesday 24 December 2003 19:00, Claudio J.
> > Margulis wrote:
> > > Does anybody understand this behavior:
> > >
> > > node1-claudiom 63 % pwd
> > > /scratch/claudiom/111
> > > node1-claudiom 64 % ls
> > > topol.tpr
> > > node1-claudiom 65 % mdrun
> > >
> > >                          :-)  G  R  O  M  A  C  S
> > (-:
> > >
> > > Segmentation fault
> >
> > You could try running mdrun through strace, if the
> > latter is available on your
> > system. (It should be present on most Linux
> > systems.)
> >
> > To do this, use "strace mdrun", which will print a
> > list of the system calls
> > mdrun uses up to the point of the segmentation
> > fault. This might provide a
> > clue as to what it is trying to do. Since it crashes
> > pretty quickly, there
> > shouldn't be too many calls to sort through.
> >
> >
> > Happy holidays to all,
> >
> > --
> > Lieven Buts
> > Department of Ultrastructure
> > Vrije Universiteit Brussel
> >
> > _______________________________________________
> > 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.
>
>
> __________________________________
> Do you Yahoo!?
> New Yahoo! Photos - easier uploading and sharing.
> http://photos.yahoo.com/
> _______________________________________________
> 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.
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O