Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one molecule, will Gromacs give the same set of force field > parameters to this molecule no matter this molecule is put in water or > in vacuum?
Depending on what's defined within the specific force field, yes. For example, ffG43b1 is a "vacuum forcefield," whereas most others are parameterized for use with condensed phases. > The bond length, the bond angle, and the dihedral angles of the same > molecule will be different in water and in vacuum. > So, will the force field parameters be changed/ adjusted in water than > in vacuum? There's no decision structure that Gromacs will magically use to determine what's in your system. All the parameters are pre-defined in the relevant .rtp and .itp files in $GMXLIB/top. > > > How does Gromacs set the force field parameters for the molecule? > I mean..... are the force field paramters determined in local or in global? > Could I change parts of the force field parameters which I found from > the published paper? The location of your files will depend on how Gromacs was installed, but can always be found in $GMXLIB/top. If you want to make changes to an existing set of parameters, it is best to copy the relevant .rtp, .itp, etc. files into your working directory and alter then there. > Or, I could not change parts of the force field parameters; instead, I > have to change the whole set of the force field > parameters??? Well, I wouldn't make random changes to things :-) The changes you make have to be compatible with the functional form and derivation of the force field. Otherwise, anything you do would probably be somewhat questionable. -Justin > > > Thank you > Lin > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
