On 4/16/15 7:33 AM, Tushar Ranjan Moharana wrote:
Hi Justin
Thanks for your valuable advice. I had a misconception that in GROMACS Just
adding NA and CL doesn't produce the effect of salt concentration.
It arises because most of the paper I have read about effect of salt
concentration on protein or DNA the structure of the bio molecule doesn't
shows any significant change (this may be also because those protein
doesn't change much with salt concentration). I read your recent paper
where you used "Drude Polarizable Force Fields" which can't be used in
GROMACS.
It will be available soon. Just waiting on reviewers to get back to us... :)
For a very explicit example of how polarizability is very important in the
context of DNA-ion interactions, see http://dx.doi.org/10.1021/acs.jpcb.5b00683
As you said that it depends on force field so I am just curious to know
which force field and water model one should use for simulating a system
(preferably protein in water) at different salt concentration to see the
effect of salt concentration on the structure of the protein.
There's lots of literature on this topic. What you choose is up to your
assessment of what might be most representative of your particular system.
-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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