Re: Reply:Re: How to convert the GROMOS parameter unit into charmm22 style

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 20 2010 - 07:50:29 CST

On Wed, 2010-01-20 at 14:05 +0100, Jérôme Hénin wrote:

> 2010/1/20 王棽 <corarbor_at_163.com>:
> > Hi, Jérôme:
> > Thank you for sharing.
> > How do you deal with the coefficient 2 in front of ^6 in NAMD's VDW
> > expression
> > "V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]"
> > while this coefficient 2 is absent in gromacs' style.

just to re-iterate. Rmin is the _minimum_ of the potential
and _not_ sigma. people often confuse these. for a 12-6
lennard-jones potential, Rmin turns out to be at 2^1/6 * sigma.

cheers,
   axel.

> >
> > best
> > Shen Wang
> >

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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