[gmx-users] structure error

David spoel at xray.bmc.uu.se
Tue Aug 31 21:49:23 CEST 2004

On Tue, 2004-08-31 at 21:03, Dinesh Pinisetty wrote:
> Hello all,
>      When I have created a bilayer and perform Energy Minimization,I was
> able to do energy minimization,but when I added water on either side and
> try to do Energy Minimization it was showing me error as "Segmentation
> Fault",Dr.David said me that generally segmentation faults are because of
> initial structures.I have checked my initial structure there was a small
> gap between water molecules and head groups they were not touching with
> each other.Could anyone guess the mistake.
You say you can do energy minimization, but does the energy go down to a
reasonable amount?

For water you should count -42 kJ/mol, for lipids even more, maybe -100
kJ/mol. Multiply by the number of molecules and check.

Do also check the components of the energy. E.g. bond and angle energies
should be small.
>        By the way I have created water molecules in two simulation boxes
> and added boxes on either side of the monolayer.
>   I hope someone would do the needful,I appreciate any help extended......
> Thanking you,
> Dinesh.
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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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