[gmx-users] Pi stacking

Justin Lemkul jalemkul at vt.edu
Thu Apr 16 14:18:14 CEST 2015

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

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 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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