[gmx-users] structure error
dpinis1 at lsu.edu
Tue Aug 31 22:57:32 CEST 2004
I said I could do energy minimization for only bilayer without water
added.When I added water it was showing me error as "segmentation fault".I
did energy minimization for only 50 ps and stopped now I want to have water
on either side of the monolayer and start energy minimization afresh of the
whole system.To start it off I should know where exactly should I work on
so that "segmentation fault error" is avoided.
Could you tell where exactly the error might be,I thought of sending you
the image of the struture to users gromacs e-mail so that you could see
that and figure out the mistake,but it does not allow me to do as the size
If you allow me I can send it to your e-mail instead of users
From:gmx-users-bounces at gromacs.org on 08/31/2004 09:49 PM ZE2
Sent by: gmx-users-bounces at gromacs.org
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cc: (bcc: Dinesh Pinisetty/dpinis1/LSU)
Subject: Re: [gmx-users] structure error
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
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
> Thanking you,
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> gmx-users at gromacs.org
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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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