Hi Art, You could, but should you? What do you think to gain? One layer of water is approximately 2.5 A, so with 6 you'd have about two layers of water 'free'. With position restraints on the rest, you'd still be calculating all forces and such, so there's not much gain there. On top of that, the two water layers without position restraints will likely be quite 'icy', giving a severe constriction of your protein dynamics. Basically, your protein dynamics will be close to nonsensical; an undefined and unrealistic restricted ensemble. Now even if you're only interested in the dynamics at an active site, consider that such dynamics is part of the whole-scale protein dynamics. It's not just filling making up most of the protein.
Cheers, Tsjerk On Fri, Oct 10, 2008 at 8:25 PM, Arthur Roberts <[EMAIL PROTECTED]> wrote: >> Hi, all, > > In a previous email, I asked about the availability of implicit water > calculations in Gromacs 4.0, which might be available in Gromacs 4.1. In > the meantime, I was wondering if I position restrained waters that are 6 > Angstroms from the protein, would that increase the speed of md simulation, > if I have a water shell that extends 15 Angstroms. I would appreciate your > input. > > Best wishes, > Art Roberts > University of Washington > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 thewww interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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
