[gmx-users] ngmx: Segmentation fault

[David]

On Fri, 2003-08-29 at 18:17, Albert Sun wrote:
> Hi, David, 
> Do you know what is the reason that atoms explod? 
> Is it because that I did not include bond force and constraints or
> other wrong parameters?
Anything, charged atoms with no van der waals or something like that.
Something in your topology. If you give all atoms zero charge and a
reasonable vanderwaals params it will work fine.
>  
> thanks!
>  
>  
>  
>    
>         David <spoel at xray.bmc.uu.se> wrote: 
>                 On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
>                 > Dear David van der Spoel,
>                 > I am testing a simple case, and prepared top and gro
>                 files as
>                 > attached, when I ran EM.mdp and 9atom.mdp, and see
>                 ngmx, it has the
>                 > error: segmentation fault.
>                 > (em.mdp file is attached in another email)
>                 > Could you help me to have a look?
>                 
>                 I see a system of 9 atoms in a plane which explodes
>                 after roughly 100 fs
>                 (I decreased nstxout to 5 to see it).
>                 
>                 If you do not see that, then I suggest you try to run
>                 it on a Linux or
>                 Unix box first. By the way, ngmx won't work on a DOS
>                 anyway.
>                 
>                 
>                 -- 
>                 Groeten, David.
>                 ________________________________________________________________________
>                 Dr. David van der Spoel, Dept. of Cell and Molecular
>                 Biology
>                 Husargatan 3, Box 596, 75124 Uppsala, Sweden
>                 phone: 46 18 471 4205 fax: 46 18 511 755
>                 spoel at xray.bmc.uu.se spoel at gromacs.org
>                 http://xray.bmc.uu.se/~spoel
>                 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>                 _______________________________________________
>                 gmx-users mailing list
>                 gmx-users at gromacs.org
>                 http://www.gromacs.org/mailman/listinfo/gmx-users
>                 Please don't post (un)subscribe requests to the list.
>                 Use the 
>                 www interface or send it to
>                 gmx-users-request at gromacs.org.
>         
>         
>         ______________________________________________________________
>         Do you Yahoo!?
>         Yahoo! SiteBuilder - Free, easy-to-use web site design
>         software
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++