[gmx-users] gmx-users] Atoms Exploded

Albert Sun albert_sun9 at yahoo.com
Thu Sep 11 17:31:02 CEST 2003

Dear Users,
When I simulated a simple 9 atoms system, simulation (mdrun) was completed,  but the .trr  picture show that atoms disappeared suddenly and can not see anything from  the first frame.
Appreciate if you could advise me how to modify (.mdp or .top or other files) so that I can  see the picture from the first frame?

Albert Sun <albert_sun9 at yahoo.com> wrote: 
Hi, David and users,
My simple case study has not shown good results, the 9atom always exploded, 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 comments 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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> ATTACHMENT part 2 application/octet-stream name=9atom.gro

> ATTACHMENT part 3 application/octet-stream name=9atom.top

> ATTACHMENT part 4 application/octet-stream name=9atom.mdp

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