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

[David van der Spoel]

On Thu, 2005-07-14 at 07:20 -0700, Tanping Li wrote:
> 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.
grompp removes the unused ones. you can have it not do that by an option
-norenum
> 
> 
> 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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> > 
> > 
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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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