Just my unasked-for two cents: Langevin dynamics in water is probably a poor substitute for some representation of water. Langevin can provide some of the friction/noise of water -- but electrostatics interactions are very different in water than in vacuum. Langevin dynamics is probably not a substitute for an implicit solvent model.
On 10/30/07, Syma Khalid <[EMAIL PROTECTED]> wrote: > > > > > Dear all, > > > > I was wondering if someone could offer some advice? > > I would like to run an atomistic langevin dynamics simulation (as I don't > want to include water explicitly). If I add the appropriate langevin > dynamics options in the mdp file, then is there any reason why I shouldn't > use explicit counter ions (unfortunately my protein has an overall charge)? > > > > Obviously I would use periodic boundary conditions so the ions don't wander > off. > > > > Many thanks in advance for your suggestions/comments, > > > > -Syma > > > > > > > *********************************************************************** > Dr Syma Khalid > RCUK Fellow (Chemical Biology) > School of Chemistry > University of Southampton > Highfield > Southampton phone: (0)2380-594176 > SO17 1BJ email: [EMAIL PROTECTED] > U.K. > *********************************************************************** > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
