Many thanks David. Just want to confirm that I understand how to calculate the monomer correctly. So I put the single molecule inside a large cubic box, say with a dimension of 10 x 10 x 10 nm^3, then I use NVT ensemble and the same cut-off parameters as the ones that I apply during my bulk simulation?
On Sun, Feb 27, 2011 at 11:34 PM, David van der Spoel <[email protected]> wrote: > On 2011-02-27 21.20, aldi asmadi wrote: >> >> Dear all, >> >> This may sound obvious and normally I would know how to address the >> following question. However, I would like to ask for your opinion. >> If we are simulating bulk liquid of hydrocarbon using the shell >> polarizable model, is it possible to have a positive value for the >> potential energy? In my simulation, for every step, the system is >> energy minimized in order to accommodate the behavior of the shell >> particles. For the shell particles, I use emtol = 0.1 and niter = >> 100. In the log file, the potential energies are mostly reported as >> positives (except in the beginning steps), but there is no line saying >> that the 'energy minimization (EM) does not converge'. >> >> I understand that if the potential energy is positive, this may >> indicate that the system is exploding. When I calculate the density, >> however, it corresponds quite well. >> >> Many thanks in advance. >> >> Regards, >> Aldi > > You should subtract the energy of a monomer in order to get the > intermolecular energy. Try computing the heat of vaporization: > > DHvap = Epot(g) - Epot(l) + kBT > > and compare it to the experimental value. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > [email protected] http://folding.bmc.uu.se > -- > 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
