Hi, You could also observe the change in e.g. free-energy of solvation of that ion in that force field upon change in temperature. Or maybe something even more relevant?
Mark On Thu, Jul 2, 2015 at 5:29 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/2/15 10:33 AM, soumadwip ghosh wrote: > > Hi, > > I am stuck with one of the reviews of my paper where i have > > investigated the thermodynamics of small molecular ion binding to DNA > > duplex using CHARMM 27 force field. In order to do so I calculated the > PMF > > of the binding processes at different temperature ( 300, 270 and 330K) > and > > then decomposed the temperature dependent PMFs to estimate the entropy > and > > enthalpy contributions respectively. One of the reviewer has strong > > objection about the validation of classical force fields beyond room > > temperature. While I know this has been a major issue in simulation of > > biomolecules (say temperature assisted protein unfolding or hydrophobic > > interactions between two methane molecules in water) and REMD may be a > > possible way out but there are examples of works such as below where > > temperature variation of force fields during a classical MD simulation > did > > not seem to be an issue or neither has been addressed by the authors. > > > > http://pubs.acs.org/doi/pdf/10.1021/jp056909r > > and > > > > http://pubs.acs.org/doi/pdf/10.1021/jp512336n > > > > I cannot perform REMD for all the ion associations at this moment and > apart > > from this comment I have satisfactorily answered the rest of the queries > of > > the referees. Is there some way by which I can convince the referee? Can > > anyone help me with some references where CHARMM force fields have been > > used without any modification to study a biomolecule beyond room > > temperature using MD simulations? In general I will be highly obliged if > > someone helps me with an appropriate response to the reviewer? > > > > There have been DNA base flipping studies that have done this, though I > don't > remember if it was with CHARMM or AMBER. In any case, an objection about > 330 K > strikes me as pretty absurd. That's not an unreasonable temperature, and > people > simulate membrane proteins in DPPC at 323 K or higher all the time and > they're > fine. You start getting into trouble at 400, 500 K, etc. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.