[gmx-users] Setting up an infinitely hard wall

Amit Choubey kgp.amit at gmail.com
Fri Oct 23 09:26:08 CEST 2009

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,

> Berk
> ------------------------------
> 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.<http://windows.microsoft.com/shop>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091023/e581ba5c/attachment.html>

More information about the gromacs.org_gmx-users mailing list