[gmx-users] g_hbond segmentation fault

[Erik Marklund]

  Hi,

Could you file a bugzilla and attach the trr and tpr files please? If 
you do I'll try to sort it out today or at least this week.

Erik

Yao Yao skrev 2010-09-29 08.22:
>
>
> 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 </mc/compose?to=spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     -- 
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>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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