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<br><br>> Subject: Re: [gmx-users] Hard Spheres<br>> From: sascha.hempel@bci.tu-dortmund.de<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 9 Dec 2010 08:56:54 +0100<br>> <br>> > On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel<br>> > <sascha.hempel@bci.tu-dortmund.de> wrote:<br>> > Hi all!<br>> > <br>> > I am trying to add some hard spheres to my simulation. As far<br>> > as i can<br>> > tell from the manual Gromacs supports only LJ or Buckingham<br>> > for<br>> > non-bonded interaction.<br>> > <br>> > <br>> > Why cant you use LJ? By setting the attractive part equal to zero.<br>> > <br>> The LJ Equation is 4 * eps * ( (sig/r)**12 - (sig/r)**6).<br>> If I either set sigma or epsilon to zero the Potential will become zero<br>> for all r<br><br>Search in the manual for combination rule 1, then you can set C6 and C12.<br>Also I just replied a week ago to a mail where a user wanted to set C6<br>to zero while supplying sigma and epsilon, you can do that by putting<br>a minus sign in front of the sigma.<br><br>Another option is using tabulated potentials (user), then you can use anything,<br>except for completely hard spheres, which would lead to infinite forces.<br><br>Berk<br><br>> > <br>> > Is there a way to add hard spheres to lets say a simulation of<br>> > Water<br>> > molecules without interfering into the regular water-water<br>> > interaction?<br>> > <br>> > Thanks a lot in advance,<br>> > <br>> > Sascha<br>> > <br>> > TU Dortmund<br>> > Laboratory of Thermodynamics<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before<br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> > <br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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