[gmx-users] help about topol.tpr file of small molecular complex

[David van der Spoel]

On Tue, 2003-06-03 at 10:51, Christoph Freudenberger wrote:
> You should consider using quantum chemistry to deal with
> that kind of problem.
> Check out programs like Spartan, Titan or Gaussian.
> 
That's a possibility, but if you have a good force field you could do it
with modelling too. Try generating topologies using the prodrg server
for both molecules individually (all-atom benzene!) and then combine
them (chapter 5 of manual).

> Rongjian Sa wrote:
> > Dear everyone:
> > I want to use gromacs to simulate the interaction between two molecules. 
> > My system contain one ammonium and one benzene molecules. I have only 
> > obtain one benzene molecule. I have attached my pdb file. So I want to 
> > know who can help me about this.
> >  
> > Sincerely yours,
> > Rongjian
> >  
> > PDBFIL pdb file created from cpmd Wannier file: ELF
> > ATOM      1 C    MOL     1      -0.001   0.620   1.405  1.00 10.00
> > ATOM      1 C    MOL     1       1.214   0.616   0.703  1.00 10.00
> > ATOM      1 C    MOL     1       1.214   0.615  -0.702  1.00 10.00
> > ATOM      1 C    MOL     1      -0.001   0.618  -1.404  1.00 10.00
> > ATOM      1 C    MOL     1      -1.215   0.623  -0.702  1.00 10.00
> > ATOM      1 C    MOL     1      -1.215   0.625   0.703  1.00 10.00
> > ATOM      2 H    MOL     1       0.000   0.643   2.494  1.00 10.00
> > ATOM      2 H    MOL     1       2.158   0.641   1.247  1.00 10.00
> > ATOM      2 H    MOL     1       2.158   0.639  -1.247  1.00 10.00
> > ATOM      2 H    MOL     1       0.000   0.639  -2.493  1.00 10.00
> > ATOM      2 H    MOL     1      -2.159   0.655  -1.247  1.00 10.00
> > ATOM      2 H    MOL     1      -2.159   0.657   1.247  1.00 10.00
> > ATOM      2 H    MOL     1       0.009  -2.971   0.845  1.00 10.00
> > ATOM      2 H    MOL     1       0.009  -2.975  -0.847  1.00 10.00
> > ATOM      2 H    MOL     1      -0.833  -1.757  -0.003  1.00 10.00
> > ATOM      2 H    MOL     1       0.821  -1.735  -0.003  1.00 10.00
> > ATOM      3 N    MOL     1       0.002  -2.382  -0.002  1.00 10.00
> 
> -- 
> Christoph Freudenberger
> Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. 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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