[gmx-users] gmx-users] Atoms Exploded

[Albert Sun]

Dear Groeten, David
How to start simple Lennard Jones particles in Gromacs?
by specify force field: ffgmx

thanks!
 
Albert
 

David <spoel at xray.bmc.uu.se> wrote:
On Sat, 2003-09-20 at 21:09, Albert Sun wrote:
> Hi, Dear Anton,
> Atoms exploded problem still remains, when I view .trr file by VMD,
> all atoms suddenly disappear.
> I tried ngmx, it had error: float exception. 
> I tried trjconv -dump, it showed warning: "no output, trajectory ended
> at 3" 
> 
> could you give me more hints ? 


It seems to me that you have just a weird system with all atoms placed
in a plane, and large forces between them.

If you intend to simulate some sort of two dimensional crystal, you
should probably start with simple Lennard Jones particles.
-- 
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
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