[gmx-users] simulations using structureless surface-2

singh singh at biophysik.chemie.uni-dortmund.de
Thu Jul 26 13:54:44 CEST 2007

Dear gmx users,
my apologies for the previous post. I will try to rephrase my problem.

Is it possible to introduce a plane in a particular direction, for example
in z direction, where molecules interact with it only based on the
perpendicular distance between the molecules and the plane?

Is it also possible to specify the user defined potential for interaction
between the plane and molecules?

The idea is to simulate a surface, for example a graphite surface, but
rather than using a detailed atomistic model for it, I would like to
represent it by using a plane with some interaction potentials. 

With Regards,
Gurpreet Singh

University of Dortmund
Department of Chemistry
Physical Chemistry I  -  Biophysical Chemistry
Otto-Hahn Str. 6
D-44227 Dortmund
Office:   C1-06 room 176
Phone:  +49 231 755 3916
Fax:     +49 231 755 3901

-----Original Message-----
From: Mark Abraham [mailto:Mark.Abraham at anu.edu.au] 
Sent: Wednesday, July 25, 2007 3:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] simulations using structureless surface

singh wrote:
> Dear Gromacs users,
> I want to simulate water in slit like pores where the pore surface can 
> be represented by a plane in z direction, interacting with water 
> molecules using 9-3 potential (or any other) but rather than using 
> particles in the surface and thus the distances between particles in the 
> surface and water, I want to use only the distance between water and 
> surface in z direction only (a structure less surface). In the mailing 
> list , I found some reference to the -glass option in mdrun but not much 
> information is available regarding it except that it is only for special 
> long range corrections.   I would like to know the possibilities of 
> simulating such systems using gromacs.

Please use one idea per sentence and describe fully what you're trying 
to do.


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