[gmx-users] g_hbond segmentation fault

[Yao Yao]

Hi Gmxers,

Sorry, Eric and David, 

I cannot transfer my trr file to report a bug because of its huge size.
It is just a regular protein with 70 Angstrom cubic TIP5P water box in Charmm27 force field. That's all of the system.

But anyway, i included the mdp file in the attachment.

Hopefully someone can help me.

Many thanks,

Yao  




--- On Wed, 9/29/10, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> From: Erik Marklund <erikm 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, 7:55 AM
> 
> 
>   
> 
>     
>   
>   
>     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 
>                       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/
> 
>   
> 
> 
> -----Inline Attachment Follows-----
> 
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