Hi,
You can try the 'randomizeions' command in ptraj/cpptraj.
-Dan
On Sunday, February 17, 2013, Sun wrote:
> Dear all,
> I want to do some molecular dynamic simulation for a protein to verify the
> hypothesis that the side chain of W286 in the protein can rotate freely.
> The protein was solvated in TIP3P water and 9 Na+ as counterions were added
> to neutralize the charge. But one Na+ was placed colsely to the W286, and
> when I checked the trajectory of the simulation I found that the side
> chain of W286 was nearly freezed via the pi-ð interaction between the
> benzene ring of W286 and the Na+, so the simulation does not do any help .
> What I want to ask is that can I move the Na+ a little further from W286
> while still keeping the system neutralized so that the counterion does not
> limit the rotation of side chian ? If I can, how to do it ? if not , is
> there anyway to solve the problem?
>
> -sun
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sun Feb 17 2013 - 12:00:02 PST
