[gmx-users] Re: gmx-users] Atoms Exploded

[Albert Sun]

Dear David and Gmx-users,
I have a few stupid questions:
How to simulate simple Lennard Jones particles in Gromacs? 
In .top file, we don't need input bond and angle data, is it right?
How to specify force field in .top file?
 
Greatly appreciate your clarification.
 
Thanks 
 
Albert
 
 
 


Albert Sun <albert_sun9 at yahoo.com> wrote:
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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