[gmx-users] Setting up an infinitely hard wall
kgp.amit at gmail.com
Fri Oct 23 09:26:08 CEST 2009
Thank you for the response.
I have obtained distributions with in infinite wall by simulating with an
> softer wall
> and unbiasing with configurations with the wall potential.
Could you explain the above ? I am not sure if i get your point.
> But if you need the dynamics, or you want less hassle during the
> 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
> of the particle in the wall.
That's true. I am sorry i didnt mention that.
> This should on require a few lines of code in do_update_md
> in src/mdlib/update.c.
Great, I will try this as soon as possible.
> Note that this will only work easily when you do not have constraints
> With constraints things get much more complicated.
I do have constraints present. Thank you for pointing this. I am working
with SPC water and I should, in principle be able to figure out the
co-ordinates of all atoms in the molecule if I am given one of the water's
atom's co-ordinate. Does that sound ok?
Thanks for the input again,
> 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
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