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
--
==================================================
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
==================================================
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