[gmx-users] gmx-users] Atoms Exploded

Albert Sun albert_sun9 at yahoo.com
Sun Sep 21 20:56:02 CEST 2003

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


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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