[gmx-users] Setting up an infinitely hard wall

Berk Hess gmx3 at hotmail.com
Fri Oct 23 09:05:09 CEST 2009


I have obtained distributions with in infinite wall by simulating with an softer wall
and unbiasing with configurations with the wall potential.
But if you need the dynamics, or you want less hassle during the simulation,
you will have to do a bit more effort in coding an infinitely hard wall.

You will not only have to inverse the velocity, but also mirror the position
of the particle in the wall. This should on require a few lines of code in do_update_md
in src/mdlib/update.c.

Note that this will only work easily when you do not have constraints present.
With constraints things get much more complicated.


Date: Thu, 22 Oct 2009 14:34:06 -0700
From: kgp.amit at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] Setting up an infinitely hard wall

Hi everyone,
I am sending this email again hoping for any quick input for my question.

I have been trying to set up an "infinitely" hard potential wall. 
I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller time step and i cant afford to have smaller time step. 

My idea to overcome this issue is to just reverse the velocity of the particle whenever it hits the wall. I am not sure if there is any thing in GROMACS which does this but any suggestions will be very helpful.

If there is nothing set up for something like above, i would like to play around with the code to figure it out. If this is the case, could somebody direct me to a starting point.

Thank you Amit

New Windows 7: Find the right PC for you. Learn more.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091023/775963c1/attachment.html>

More information about the gromacs.org_gmx-users mailing list