Hi,
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.
Berk
Date: Thu, 22 Oct 2009 14:34:06 -0700
From: kgp.a...@gmail.com
To: gmx-users@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
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