[gmx-users] Setting up an infinitely hard wall

Berk Hess gmx3 at hotmail.com
Fri Oct 23 10:09:24 CEST 2009


If you have a wall potential, you can reweight the configurations
with weight 0 if one or more particles are beyond the wall
and exp(Vwall/kT) if no particles are beyond the wall.
This will only work efficiently if you choose the wall potential in a smart way.
I managed to get an efficiency of 70%.

If you have constraints, an atom that goes beyond the wall is directly
coupled to the atoms it is constrained to. You will have to work out
the equations for such a situation. It might be as simple that you can
just correct x and v for the atom that went beyond the wall and then
apply the constraints as normal.


Date: Fri, 23 Oct 2009 00:26:08 -0700
Subject: Re: [gmx-users] Setting up an infinitely hard wall
From: kgp.amit at gmail.com
To: gmx-users at gromacs.org

Hi Berk,
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 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. 
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 present.
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,Amit 

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

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