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

[Anton Feenstra]

Albert Sun wrote:
> Dear David and Gmx-users,
> I have a few stupid questions:
> How to simulate simple Lennard Jones particles in Gromacs? 

something like:

[ atomtypes ]
LJ <parameters>

[moleculetypes]
1 LJ <parameters>

[system]
Simple LJ particles

[molecules]
LJ	1

Check the manual to see what needs to be specified in each of the
sections, I might also have left out some obligatory sections (like
[defaults]).

> In .top file, we don't need input bond and angle data, is it right?

Right.

> How to specify force field in .top file?

Define your own [atomtypes] (as above), or #include ff<FF>.itp, where <FF>
would be something like 'gmx', 'G43a1', 'OPLS??'). N.B. you don't need
any of the .atp, .rtp., .hdb, .tdb files (these are for pdb2gmx only).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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