[gmx-users] segmentation fault

[David]

On Tue, 2004-08-17 at 18:08, Dinesh Pinisetty wrote:
> 
> 
> Dear Dr.Berk,
>         I tried with having 0.9 for rlist and rcoulomb,1.4 for rvdw.It did
> not work for me either.At step 0 itself it says segmentation fault.My
> topology file has shows that 5409 water molecules are added along with 96
> molecules of DPPC.As Dr.David said I tried to do energy minimization with
> only DPPC molecules without water molecules even then I got at step 0 the
> same error "SEGMENTATION FAULT".
>      I do not understand what the problem is?As a beginner to GROMACS I
> tried everything with little knowledge I have,Please let me know with your
> experience what should I test for to checkout the error........

Maybe it's time to start from scratch.

1. (Install gromacs 3.2.1 if you haven't already).
2. First build and minimize a single DPPC molecule
3. Use genconf to multiply the conformation to a monolayer of 48 (e.g.
genconf -f confin -nbox 8 6 1 -o conf_48). Take care that there is
enough space between the molecules.
4. Use editconf to rotate and translate the conf_48 file 
(e.g. editconf -f conf_48 -scale 1 -1 -1 -o conf_48_2 -translate 0 0 5)
5. Use emacs to merge the two files (check box size and number of atoms)

Then minimize the whole system as described before.


> Thanking you,
> Dinesh.
> 
> 
> 
> 
> 
> 
> From:gmx-users-bounces at gromacs.org on 08/17/2004 10:22 AM ZE2
> 
> 
> Sent by: gmx-users-bounces at gromacs.org
> 
> Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
> 
> 
> To:   gmx-users at gromacs.org
> cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)
> 
> Subject:    Re: [gmx-users] segmentation fault
> 
> 
> 
> 
> 
> 
> >From: Dinesh Pinisetty <dpinis1 at lsu.edu>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] segmentation fault
> >Date: Mon, 16 Aug 2004 11:38:44 -0500
> >
> >
> >
> >
> >
> >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.
> 
> 0.5 nm for rcoulomb and rlist is far too short.
> You probably want to have all cut-off's, including rvdw at 0.9.
> The same problem came up in the "pme + barostat" mails
> a few days ago.
> 
> Berk.
> 
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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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