On a related note, I remember reading a paper recently, where they take a few shells of water molecules with full atomicity, but "continuum" beyond that. They also took care about the exchange between the "molecular" water shell and the continuum as the polymer/protein conformation changes during the simulation. I have no idea how computationally efficient that would be though.
Regards, Suman. Tsjerk Wassenaar wrote: > 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 >> >> -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ 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
