[gmx-users] Pi stacking

Tushar Ranjan Moharana tusharranjanmoharana at gmail.com
Thu Apr 16 13:34:02 CEST 2015

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

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.

Thanks a lot for your time and advice.
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB

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