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 Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 ------------------------------------------------- -----Original Message----- From: Mark Abraham [mailto:[EMAIL PROTECTED] 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. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
