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

[Semen Esilevsky]

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
> 
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