[gmx-users] g_hbond segmentation fault

[Erik Marklund]

  ... and assign the bug to me please.

Erik

Erik Marklund skrev 2010-09-29 09.55:
> 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/


-- 
-----------------------------------------------
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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