[gmx-users] Temperature variation of CHARMM force field

Justin Lemkul jalemkul at vt.edu
Fri Jul 3 17:50:14 CEST 2015

On 7/3/15 2:09 AM, soumadwip ghosh wrote:
> Dear Justin and Mark,
>                                I have written a  tentative reply to the
> reviewer
> where I have mentioned the works ( DPPC membrane, protein unfolding
> and so on) where different objectives have been met with upon varying
> concentrations and it seems that the force fields just do fine. The
> papers I have cited does not contain any force field validation or
> modification by the authors while the temperature under study ranges
> from 270K to 400K. I have made a comment that a delta T = 30K is
> probably a very small temperature difference and the force field
> parameters are unlikely to get affected. In order to proove that
> reasonably good ensambles are reproduced at my simulation temperatures
> do you think I should report some of the parameters as Mark suggested
> and show that they are indeed converged in these temperatures. What I
> have in mind is I can show the density of the system after the NPT run
> since I know these values are close to each other within the given
> error bar. I used simulated annealing method for slowly
> heating/cooling the system and hence stepwise attenuation of the
> desired temperature was never a problem. Do you think if I provide
> snapshots of my density profile it will be a valid point in connection
> with the comment from the reviewer? If this is the case, is it the
> npt.edr or the md.edr file where I should look for the density? Any
> opinion regarding this would be of great help.

Density doesn't prove much, and it actually *should* vary as a function of 
temperature, inasmuch as the water model can actually respond to temperature.

Mark's suggestion for ion hydration free energy is a good one, as would RDFs of 
water around relevant functional groups to show that the hydration structure is 
not significantly perturbed.  Interaction energies might also be illustrative.



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


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