[gmx-users] truncated LJ potential

[Berk Hess]

> Date: Mon, 10 Jan 2011 14:04:34 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] truncated LJ potential
> 
> On 2011-01-10 13.39, Makoto Yoneya wrote:
> > Dear GROMACS experts:
> >
> > I'd like to use a modified Lennard-Jones potential (smoothly truncated at
> > only the repulsive part) in the following.
> >
> > V(r)
> >    = 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 - (1/4) } for r<=
> > 2^(1/6)*sigma
> >    = 0 for r>  2^(1/6)*sigma
> >
> > Which routine should I change to realize this LJ potential modification
> > without any side effects.
> > I'd like to use this in some coarse-grained simulations.
> > Sorry if this is a FAQ.
> >
> > Thank you for advance.
> >
> > Makoto Yoneya, Dr.
> > AIST, Tsukuba
> > JAPAN
> > http://staff.aist.go.jp/makoto-yoneya/
> >
> Dear Makoto,
> 
> please look into gromacs' table potential functionality, it is described 
> in the manual, and you won't have to program anything
> UNLESS the sigma is different for different atom pairs, in that case I'm 
> not sure if it will work.


You can make different tables for interactions between groups of atoms with
different sigma's by putting these groups in different energy groups,
but this might get tedious.
You can also set the environment variable nb_generic.c and modify
src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat
slower simulations.

Berk

 		 	   		  
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