[gmx-users] segmentation fault

[Dinesh Pinisetty]

Hi,
  Could anyone check out the mdp file which I am sending,When I am running
grompp I am not getting any errors or Warnings except one related to 1 atom
name which I think is very minor(It syas that its taking atom name of
topol.top into accout instead of a mismatch found in .gro file).
 I really appreciated any help extended...........
Thanking you,
dinesh.

From:gmx-users-bounces at gromacs.org on 08/15/2004 11:45 AM 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] segmentation fault



On Sat, 2004-08-14 at 22:42, Dinesh Pinisetty wrote:
>
>
> Hello everyone,
>         when I was trying to do energy minimization of
> DPPC membrane with water I am getting error as
> "SEGMENTATION FAULT".
>   I have added water using genbox command,box is
> cubic.
>   Could anybody tell me what might be the reason for
> this error...................

Could be due to large forces. In fact, almost all SEGV in mdrun are due
to large forces, i.e. non-physical coordinates. This fits well with the
way you built the starting structure.

If you insist on building your own, you might want to start with running
without water, equilibrate and add water after that.

> Thank you.
>
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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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