[gmx-users] Walls & table-based potentials
gmx3 at hotmail.com
Mon Jun 4 11:13:09 CEST 2007
Hmm, I had different problems.
In my case all energies and forces were zero.
I have fixed a bug. Do cvs update, I hope it works correctly then.
Note that you should use the new table files with V and -V' iso V and V''
>From: "Brett Olsen" <brett.olsen at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Walls & table-based potentials
>Date: Fri, 1 Jun 2007 11:35:10 -0500
>I am trying to use the new walls feature in the CVS version of
>gromacs. My system is a simple box of SPC water. When using
>with appropriate atomtype and density parameters, I have no problems,
>and the runs proceed normally.
>However, when I try to use
>I obtain segmentation faults from the md_run program. These faults
>only occur when an atom of my simulation crosses into the table-lookup
>area, within 2nm of one of the walls. So I can postpone the fault by
>adding 2nm or more of vacuum on either side of my simulation box, but
>as soon as a water molecule escapes, the program crashes. I have
>tried changing the timestep, temperature, and pressure coupling with
>I have also tried several different tables: the original table with
>the potential I am trying to use, the various table6-*.xvg tables from
>the /top directory, appropriately renamed, as well as a blank table,
>containing only zeros in all but the first, index, column. All of
>them fail in precisely the same fashion.
>Have you any advice on what could be causing this problem? I presume
>it must be related to the table itself, but I am at a loss as to how
>to fix it.
>Thank you all kindly,
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