[gmx-users] segmentation fault

[Dinesh Pinisetty]

Dear Dr.Steffen,
         Did you try on DPPC membrane.The DPPC membrane I have is the one I
generated on my own taking single molecule of DPPC.
          I tried changing gen_vel to yes,even then it shows error as
"segmentation fault".If you could specify on what molecules it worked
atleast till 200 steps I will try again.Anyways Thanks for your
reply.........
I would be grateful if you could be more specific about your
tests.............
Thanks a lot..
Dinesh...




From:gmx-users-bounces at gromacs.org on 08/17/2004 09:38 AM ZE2


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To:   gmx-users at gromacs.org
cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)

Subject:    Re: [gmx-users] segmentation fault



Hallo!
After some minor experiments with your mdp-file I have to say that it
didn't work with one of my gro/top files either. So I started adjusting
parameters. The point that stopped the error on my machine was
changing gen_vel from "no" to "yes".
Adjusting the temperature for which the velocities are generated to 0.1
made the error occur a little bit later (step 200 instead of step 30).
It didn't occur at all within the 50ps with the original 298K.
I don't know exactly how this influences the simulation setup in a way
that could cause an error but I am not an expert and I never worked
with PME before. So  you might considder someone else's
experiences.
I hope this is of some help!

Steffen

On 16 Aug 2004 at 11:38, Dinesh Pinisetty wrote:

>
>
>
>
> 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
>
>
> Sent by: gmx-users-bounces at gromacs.org
>
> Please respond to Discussion list for GROMACS users
<gmx-users at gromacs.org>
>
>
>
> 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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Steffen Härterich
Emil Fischer Centrum
FAU Erlangen-Nürnberg
Schuhstr. 19, 91054 Erlangen
Tel.: 09131/85-24111


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