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

[Jason de Joannis]

> Date: Thu, 14 Jul 2005 10:26:32 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] How to get the c12 in LJ?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1121329593.13311.0.camel at vangogh>
> Content-Type: text/plain
>
> 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

I believe i and j refer to types rather than atoms. To obtain
the type of atom k use "top->atoms.atom[k].type". Note the
definition in forcerec.h

#define C12(nbfp,ntp,ai,aj)    (nbfp)[2*((ntp)*(ai)+(aj))+1]

> > 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.

/Jason DeJoannis