[gmx-users] g_hbond segmentation fault

Yao Yao yao0o at ymail.com
Wed Sep 29 08:22:32 CEST 2010

I tried without -dt or -e, still the same problem exists in either case.

--- On Wed, 9/29/10, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] g_hbond segmentation fault
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, September 29, 2010, 6:11 AM

On 2010-09-29 08.02, Yao Yao wrote:
> Hi Gmxers,
> I used the command line,
> g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1
> and I got the message like,
try without the -dt 1

> ----------------------------------
> Found 1048 different hydrogen bonds in trajectory
> Found 2292 different atom-pairs within hydrogen bonding distance
> Merging hbonds with Acceptor and Donor swapped
> 2/10915 *Segmentation fault*
> __________________________________
> Anyone knows what could be the reason for this Segmentation Fault ?
> A couple of Q's I am also curious,
> why do we need to swap Acceptors and Acceptors when merging hbonds?
> Does gromacs suggest that the number of different hydrogen bonds in
> trajectory
> should be the same as that of different atom-pairs within hydrogen
> bonding distance?
> Thanks,
> Yao

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100928/1bcc82d9/attachment.html>

More information about the gromacs.org_gmx-users mailing list