On Thu, 2010-12-09 at 09:11 +0100, Berk Hess wrote: > > > > Subject: Re: [gmx-users] Hard Spheres > > From: [email protected] > > To: [email protected] > > Date: Thu, 9 Dec 2010 08:56:54 +0100 > > > > > On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel > > > <[email protected]> wrote: > > > Hi all! > > > > > > I am trying to add some hard spheres to my simulation. As far > > > as i can > > > tell from the manual Gromacs supports only LJ or Buckingham > > > for > > > non-bonded interaction. > > > > > > > > > Why cant you use LJ? By setting the attractive part equal to zero. > > > > > The LJ Equation is 4 * eps * ( (sig/r)**12 - (sig/r)**6). > > If I either set sigma or epsilon to zero the Potential will become > zero > > for all r > > Search in the manual for combination rule 1, then you can set C6 and > C12. > Also I just replied a week ago to a mail where a user wanted to set C6 > to zero while supplying sigma and epsilon, you can do that by putting > a minus sign in front of the sigma. > > Another option is using tabulated potentials (user), then you can use > anything, > except for completely hard spheres, which would lead to infinite > forces. > > Berk >
Thanks for your advice. I looked this up in the manual and experimented a little with the functions. I can not just set C6 to 0 beacause then i will keep a repulsing potential at long distances which will skrew with my system. I could use a shift or switch function to take care of that, but since i want some regular water in my system too this is not an option. So I am going to go with tabulated potentials. How "soft" do my hard spheres have to be to not cause any trouble for the gromacs engine? Sascha > > > > > > Is there a way to add hard spheres to lets say a simulation of > > > Water > > > molecules without interfering into the regular water-water > > > interaction? > > > > > > Thanks a lot in advance, > > > > > > Sascha > > > > > > TU Dortmund > > > Laboratory of Thermodynamics > > > -- > > > gmx-users mailing list [email protected] > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [email protected]. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
