Hello David, I send answer to the gromacs mailing list also.
12 apr 2010 kl. 17.51 skrev David Caplan: > I am still experimenting with the CHARMM27 support in Gromacs. I am > using a very recent git version (from last week). > > Currently, I'm trying to equilibrate a membrane bilayer with virtual > sites. The membrane is DPPC with the Sonne et al. parameters (for zero > surface tension): > Sonne et al. Reparameterization of all-atom > dipalmitoylphosphatidylcholine lipid parameters enables simulation of > fluid bilayers at zero tension. Biophys J (2007) vol. 92 (12) pp. > 4157-67 > > I am not so familiar with vsites, but I have read the documentation > and I saw you used vsites in your recent paper. Have you used vsites > with membrane simulations using CHARMM27? No, I have not but it should be straight forward. > If so, what kind of pressure > coupling do you use? is any surface tension applied? > If you have an example MDP that you used for this I would love to take > a look at it. I would use semiisotropic Berendsen for equilibration and perhaps switch to Parrinello-Rahman during production but when it comes to surface tension and CHARMM simulations I'm afraid I don't have any experience. Guess you have to read the cited paper carefully to figure this out. > > Also, do you typically run your CHARMM27 simulations using Langevin dynamics? No, not when you have explicit solvent. /Pär -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
