[gmx-users] gmx-users] Segmentation fault

Albert Sun albert_sun9 at yahoo.com
Tue Sep 9 19:24:00 CEST 2003

Hi, David and users,
My simple case study has not shown good results, the 9atom always explod, even though I tried many times to adjuster various parameters.
Greatly appreciate if you could help me to have a look on these files and find out where is the problem?  the following commnets are used: 

grompp -v -f em.mdp -c 9atom.gro -o em.tpr -p 9atom.top

mdrun -v -s em -o em -c afterem

grompp -f 9atom.mdp -o s1 -c afterem.gro -p 9atom.top -n atom.ndx

mdrun -s s1.tpr -o s1.trr -c s1.gro -pi pull.ppa -pn atom.ndx

(I attached three files here, three more files are attached in another mail)

David <spoel at xray.bmc.uu.se> wrote:
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 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

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