On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Sai Pooja wrote: > >> Hi, >> I want to change the non-bonded parameters to modify the interaction >> between water molecules and protein molecules. >> I am using CHARMM forcefield with Tip3p water. >> The ffnonbonded.itp file of the forcefield has non-bonded parameters for >> tip3p water. Can I achieve the above by changing these parameters? >> >> > > That depends on your definition of "modify," but yes, in a way, you can > make changes here. 1) Modify - Multiply sigma and epsilon by a constant > If yes, will this also change the non-bonded parameters for water - water >> interaction? >> > 2) Is there a way to add a new ifdef perhaps such that a modified sigma and epsilon can be used for water-protein interactions and the unmodified parameters can be used for water-water interactions? Pooja > >> > > Yes. > > -Justin > > > Pooja >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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