> Dear Amber people, I was wondering if anyone of you can give me some
> hints regarding the following issue.
As we've received four e-mails to the reflector on this issue, I assume
you really would like an answer...
> I am currently using AMBER to simulate pure molecular and ionic
> liquids, and I confront the simulation results (mainly radial
> distribution functions, etc) with X-Ray diffraction data.
> I would like to extend my analyses to spatial distribution functions
> (i. e. of cations around anions, or polar groups in molecular
> liquids), and I thought about using the grid command in ptraj to do
> that. It read in the literature that it is normally been used to
> visualize the distribution of water around solutes, e. g. proteins,
> but in principle, I think that the method could be used also in my
> case. Now the main point: in the SDF method (A. Vishnyakov, JPC A,
Correct.
> 105, 2001, 1702), implemented, e. g. in mdynamix and gromacs tools,
> the user needs to define the coordinate system for the calculation.
> What happens with ptraj? Has anybody ever done a similar type of
> calculation?
The coordinate system is already defined your x, y, z space with the grid
built around the box center (or origin). To look at the distribution
around a particular molecule or solute, you need to put that solute at the
origin. So, to look at the distribution around residue 1 we center and
image around residue 1 and if the molecule is not spherically symmetric
(like a protein) we would RMS fit to put all of the solute molecules of
interest into a common frame of reference.
The grid command below builds a 50Ax50Ax50A grid at 0.5A spacing binning
water oxygen positions. One silly issue is that the (Xplor formatted)
grids are integer based so go from -50->+49 so we need a reference
structure that is in the same frame of reference for visualizing. Here I
created this by the average command after translating back 1/2 grid
spacing.
center :1 mass origin
image origin center familiar
rms first out rms.dat :1
grid wat.grid 100 0.5 100 0.5 100 0.5 :WAT.O
translate x -0.25 y -0.25 z -0.25
average avg.pdb pdb
To do this averaged over ALL solutes (i.e. for all the ions
simultaneously) is not built in. One could in principle construct a grid
for each ion separately and then combine via some Perl or other script or
alternatively alter the code. However, given sufficient statistics
(trajectory length) the single ion grid should be representative. Try it
out and let me or the list know of troubles.
--tec3
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Received on Thu Sep 22 2011 - 11:30:05 PDT
