RE: [gmx-users] Hard Spheres
Subject: Re: [gmx-users] Hard Spheres From: sascha.hem...@bci.tu-dortmund.de To: gmx-users@gromacs.org Date: Thu, 9 Dec 2010 08:56:54 +0100 On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de 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 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Hard Spheres
On Thu, 2010-12-09 at 09:11 +0100, Berk Hess wrote: Subject: Re: [gmx-users] Hard Spheres From: sascha.hem...@bci.tu-dortmund.de To: gmx-users@gromacs.org Date: Thu, 9 Dec 2010 08:56:54 +0100 On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hard Spheres
On 09/12/10 09:51, Sascha Hempel wrote: 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? Test different function shapes -it's not easy, and also it depends on your temperature and desired time step. The smaller the time step, the steeper/hotter you can go, but of course at the price of slower simulations. I had the same issue and I used a combination of Morse potentials, a rigid one for the repulsive part and a softer one for the attractive basin (I need one as well, you maybe don't). m. 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Hard Spheres
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. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hard Spheres
On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de 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. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Hard Spheres
On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de 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 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
