The default density value in cpptraj is for water in molecules / Ang^3
(from 1.0 g/mL), so if your solvent is methanol this is not going to be
correct. The 'volume' keyword determines an average density based on the
average volume of your system (which takes everything you specify in both
masks into account). It seems like you should use the density for methanol
at whatever temperature you are simulating at, making sure you convert it
to units of molecules/Ang^3.
-Dan
On Wed, Jun 17, 2015 at 2:32 AM, Robin Jain <robinjain.chem.gmail.com>
wrote:
> Dear all amber users,
> i have a organic molecule with atomic mass 180 in methanol ( atomic mass
> 32) and i want to calculate radial distribution function. Now if used
> (a) volume keyword then i got different value on y axis
> (b) density keyword then i got different value on y axis . For example i
> used density value = 0.6022/32 = 0.01881875, when i used this density value
> for intersolvent rdf i got good result but when i used this density value
> i got very poor result, then what should density value i used for rdf
> between solute and solvent mask. Should it be 0.6022/180 or 0.6022/32 or
> other.
>
> thanking You.
>
>
> --
> Robin Jain
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jun 17 2015 - 08:00:03 PDT
