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 > > 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 > > > ------------------------------ > New Windows 7: Find the right PC for you. Learn > more.<http://windows.microsoft.com/shop> > > _______________________________________________ > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php