[AMBER] implicit models for other solvents and non-standard solvents

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Fri, 1 Dec 2017 18:05:11 +0530

Dear Amber users and developers,
I have a requirement to simulate a small molecule (139 heavy atoms) in
different solvents like heptane, methanol, and dcm.
AMBER allows simulation in water, MeOH and CHCl3, which doesn't meet our
requirements completely.

Therefore, is it possible to change the dielectric constant used in
implicit solvent MD simulations such that they are equivalent to heptane,
methanol, and dcm?

I assume that developing non-standard solvent within AMBER will require
some sort of validation with experimental data like solvent density and ?.
(These are beyond my scope at present). (
http://archive.ambermd.org/200309/0075.html)

The thread below doesn't talk about such a validation, is it necessary?
http://archive.ambermd.org/201211/0214.html

Your suggestions are highly appreciated.
thank you.

-- 
With Regards.
Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK and
IISc, Bangalore
, MRSC
)
Associate Professor,
Department of Pharmaceutical Chemistry,
School of Pharmacy & Technology Management,
SVKM's NMIMS,
Mukesh Patel Technology Park
Babulde, Bank of Tapi River,
Mumbai-Agra Road,
Shirpur, Dist. Dhule -425405
India.
Email: vaibhav.dixit.nmims.edu
www.nmims.edu
http://pharmacy-shirpur.nmims.edu/faculty-and-research/faculty/dr-vaibhav-dixit/
+91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Fri Dec 01 2017 - 05:00:03 PST