Thanks Justin. Will try to use CHARMM36 with TIP3P watermodel. On Sat, Oct 28, 2017 at 11:57 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 10/28/17 5:49 AM, Archana Sonawani-Jagtap wrote: > >> Dear all, >> >> I have used SPC water model with CHARMM27 forcrfield for performing 100ns >> protein-DNA simulation instead of TIP3P. I wanted to know if SPC water >> model can affect my simulation results in anyway considering many charged >> residues. >> > > Yes, it certainly is. CHARMM specifically balances water interactions > assuming CHARMM-modified TIP3P (with LJ on H atoms) to target individual QM > water interactions. If you change the water model, you potentially > imbalance the entire force field. The water model should generally be > viewed as an integral part of the force field, unless one does a complete > validation that the change in water model does not negatively impact the > target data (water interactions, hydration free energies, helix-coil > equilibrium, etc). > > CHARMM36 is also superior to CHARMM27 and I recommend you use it instead, > particularly if you care about subtle aspects of the DNA structure. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.