[gmx-users] Walls & table-based potentials

Berk Hess 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
>Hello everyone,
>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
>wall_type: 9-3
>wall_type: 10-4
>with appropriate atomtype and density parameters, I have no problems,
>and the runs proceed normally.
>However, when I try to use
>wall_type: table
>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
>no success.
>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,
>Brett Olsen
>gmx-users mailing list    gmx-users at gromacs.org
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Talk with your online friends with Messenger 

More information about the gromacs.org_gmx-users mailing list