[gmx-users] LJ cut-off distance

[Mark Abraham]

On 23/10/2010 2:08 AM, C. Batistakis wrote:
> Dear Justin
>
> Actually, what I want to do is to kill the attraction part of the LJ 
> substrate-polymer interaction. So, I was thinking to put the cut-off 
> equal the 1,12σ (point with the lowest energy).
>

Mentioning the real objective, as well asking about a form of its 
solution is often productive :-)

>
> Do you have any other idea how can I have only the repulsion part?
>
> If not, can you suggest me a further reading about how to use 
> tabulated potentials?
>

http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials and 
several places in the manual.

I think you want to use energy group tables, and to modify the 
functional form for only substrate-polymer energy group.

Mark

>
> -Many thanks, Chrysostomos
>
> --- Στις *Παρ., 22/10/10, ο/η Justin A. Lemkul /<jalemkul at vt.edu>/* 
> έγραψε:
>
>
>     Από: Justin A. Lemkul <jalemkul at vt.edu>
>     Θέμα: Re: [gmx-users] LJ cut-off distance
>     Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Ημερομηνία: Παρασκευή, 22 Οκτώβριος 2010, 17:51
>
>
>
>     C. Batistakis wrote:
>     > Dear all
>     >
>     > I have a system of polymer chains between 2 substrates. The
>     substrates are FCC lattices consisting of Lennard-Jones particles.
>     > I would like to know if it’s possible to handle individually the
>     cut-off distances of the LJ interactions in the system
>     >
>     > For example, I would to use one cut-off distance for the LJ
>     interactions between the particles of the substrate but a
>     different cut-off distance for the LJ interaction between the
>     substrate and the polymers. Is this possible?
>     >
>
>     No.  There can be only one value of rvdw.  If you want custom
>     potentials, you can use tabulated potentials, but I don't think
>     this directly addresses what you want to do.
>
>     -Justin
>
>     > Many thanks in advance
>     >
>     > Chrysostomos
>     >
>     >
>
>     -- ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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