[gmx-users] temperature variation of all-atom CHARMM force fields

[Mark Abraham]

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 <jalemkul at 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
>
> jalemkul at 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-request at gromacs.org.
>