[gmx-users] How to get the c12 in LJ?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jul 14 10:26:32 CEST 2005
On Wed, 2005-07-13 at 14:57 -0700, Tanping Li wrote:
> Hellow, everyone,
> I am calculating the LJ interaction between protein
> residue and some close waters. I noticed that
> c12(i,j)=sqrt(c12(i,i)*c12(j,j)) is not always true in
> some situations, which is also mentioned in previous
> messages. So where can I get the c12 that gromacs
In the tpr file, there is a matrix (look for idef when you gmxdump it).
The matrix is stored linearly like 0,0 0,1, 0,2 ... 1,0 1,1 ... n-1,n-1
> I have struggled for several days and hope your reply.
> Thank you very much.
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David van der Spoel, PhD, Assoc. 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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