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Hi,<br><br>If you have a wall potential, you can reweight the configurations<br>with weight 0 if one or more particles are beyond the wall<br>and exp(Vwall/kT) if no particles are beyond the wall.<br>This will only work efficiently if you choose the wall potential in a smart way.<br>I managed to get an efficiency of 70%.<br><br>If you have constraints, an atom that goes beyond the wall is directly<br>coupled to the atoms it is constrained to. You will have to work out<br>the equations for such a situation. It might be as simple that you can<br>just correct x and v for the atom that went beyond the wall and then<br>apply the constraints as normal.<br><br>Berk<br><br><hr id="stopSpelling">Date: Fri, 23 Oct 2009 00:26:08 -0700<br>Subject: Re: [gmx-users] Setting up an infinitely hard wall<br>From: kgp.amit@gmail.com<br>To: gmx-users@gromacs.org<br><br>Hi Berk,<div><br></div><div>Thank you for the response.<br><br><div class="ecxgmail_quote"><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>I have obtained distributions with in infinite wall by simulating with an softer wall<br>
and unbiasing with configurations with the wall potential.<br></div></blockquote><div><br></div><div>Could you explain the above ? I am not sure if i get your point.</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>But if you need the dynamics, or you want less hassle during the simulation,<br>you will have to do a bit more effort in coding an infinitely hard wall.<br><br>You will not only have to inverse the velocity, but also mirror the position<br>
of the particle in the wall. </div></blockquote><div><br></div><div>That's true. I am sorry i didnt mention that.</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>This should on require a few lines of code in do_update_md<br>in src/mdlib/update.c.<br></div></blockquote><div><br></div><div>Great, I will try this as soon as possible. </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><br>Note that this will only work easily when you do not have constraints present.<br>With constraints things get much more complicated.<br></div></blockquote><div><br></div><div>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?</div>
<div><br></div><div>Thanks for the input again,</div><div>Amit</div><div> </div><blockquote class="ecxgmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br>Berk<br><br><hr>Date: Thu, 22 Oct 2009 14:34:06 -0700<br>
From: <a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] Setting up an infinitely hard wall<div>
<div></div><div class="h5"><br><br><div>Hi everyone,</div><div><br></div><div>I am sending this email again hoping for any quick input for my question.</div><div><br></div><div>
<br></div><div><div><br></div><div>I have been trying to set up an "infinitely" hard potential wall. </div><div><br></div><div>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. </div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div>
<div>
Thank you </div><div>Amit</div>
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