Hi Stephane, > I am doing some tests with the CHARMM port in GROMACS. Before to start > more extensive simulations with this ff > I have performed a short run of 1000 TIP3-CHARMM water molecules in a > cubic during at T=300 K and P=1.015 bar with v-rescale and PR as > thermostat and barostat. I have used the VERSION > 4.0.99_development_20090927 of GMX.
good to hear that you could reproduce our results. > > Moreover, since I am not a power user of GROMACS, I don't know how to > translate in GROMACS directives the sentence given in JCTC paper " using > a short-range cutoff of 1.2 nm, and van der Waals interactions were > switched off between 1.0 to 1.2 nm". This means coulombtype = PME, rcoulomb = 1.2, vdw-type = switch, rvdw-switch = 1.0, rvdw = 1.2. > And by consequence what are the > corrects coulomb and vdw parameters for simulations of CHARMM ff ? This you should be able to figure out from the CHARMM ff papers. According to the CMAP paper (MacKerell et al. Journal of Computational Chemistry 2004) they used real-space (short-range) cutoff of their electrostatic calculations (using PME) of 8.5 Å, and the LJ were switched of between 7.5 to 8.5 Å and their neighbor lists had a cutoff of 10.5 Å. Remember that we performed the testing (comparing the energy terms) in the paper without cut-offs. /Pär-- 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
