[gmx-users] structure error

[Dinesh Pinisetty]

Dear Dr.David,
      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
will exceed.
     If you allow me I can send it to your e-mail instead of users
list.........
Thanking you,
Dinesh.


From:gmx-users-bounces at gromacs.org on 08/31/2004 09:49 PM ZE2


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To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
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
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.
________________________________________________________________________
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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