[gmx-users] How to get the c12 in LJ?

[Tanping Li]

Thank you very much for the reply. But there are only
over 200 items in idef. How are they ordered? What
does n mean here? Because there are about 50 atom
types in the ***.atp file.


Best
Tanping

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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
> > uses?
> 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.
> > 
> > 
> > Best
> > Tanping
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> -- 
> David.
>
________________________________________________________________________
> 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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