[gmx-users] g_hbond segmentation fault

[Yao Yao]

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

--- 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
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