[gmx-users] structure error

[David]

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.
> 
> _______________________________________________
> 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++