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

soumadwip ghosh soumadwipghosh at gmail.com
Thu Jul 2 18:56:46 CEST 2015

Dear Justin and Mark,
                              I have written a 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.

Thanks and regards,
Soumadwip Ghosh
Research Fellow

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