[gmx-developers] calculating LJ (SR)

[David]

On Mon, 2004-02-16 at 07:17, Ranjit Sudhakar Ranbhor wrote:
> Hi,
> 
> I am calculating LJ potential (SR ie 1-5 and onwards) in one small
> program. While doing so I am using C6 and C12 parameters given under [
> nonbond_params ] in file ffG43a1nb.itp. I think under nonbond_params all
> combinations are not present. I am getting less energy (85% of Gromacs)
> than Gromacs calculated energy. Is there any rule for combination or I can
> simply make all combinations for C6 and C12?
First make a matrix from what's under [ atomtypes ] then overwrite the
matrix elements with [ nonbond_params ]. The procedure is coded
somewhere in grompp:
topio.c:            generate_nbparams

Alternatively you can just read a tpr file using gromacs routines.

> 
> Regards,
> 
> Ranjit Ranbhor
> Research Scholar
> Indian Institute of Technology-Bombay
> Biotechnology Group
> School of Biosciences and Bioengineering
> Powai, Mumbai 400076
> India
> Tel.:+91-22-25764780
> Web: http://www.btc.iitb.ac.in/~ranjit
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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