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Re: WSN: Explicit pair distances (fwd)
Sender: bruce_bush@merck.com (Bruce Bush)
Subject: Re: WSN: Explicit pair distances
I don't know how MDANAL works, but you might be able to do the following
with minimal awk'ing, using AMBER or MDANAL to do the distance calcs as part of
its normal energy calcs:
turn off all energy terms except electrostatics
if possible, turn "off" the charge on water hydrogens
set up a sharp truncation of nonbonds at, say, 16A
read trajectory, accumulate energy (solute-solvent electrostatic)
per solute atom; save results (a list, one energy per atom)
change truncation to 15A
read trajectory, accumulate, save results
change truncation to 14A
. and so forth...
When done, combine and process the output lists (with paste and awk).
The desired histogram results from differences in adjacent energies.
Divide the difference by solute charge and multiply by (r_midpoint) or
(r_mid**2), unless what you wanted in the first place is a histogram
of interaction energies.
bruce_bush@merck.com in one of his sneakier moods ...
-------------------------------------------------
> I am interested in analyzing some MD simulations with explicit solvent. The
> main thing I want to is to plot the pair distribution function for each polar
> solute atom with respect to all water oxygens. AMBER's MDANAL program will
> only give me the average distance during the simulation, but I'm interested in
> each distance at each time-step(for which I have the coordinates)
>
> Does anyone have any software for doing this? ...
>
> ---------------------------------------------------------------------
> Brad Isbister Duke University
> longshot@chem.duke.edu Department of Chemistry
> Computational/Biophysical chemistry E.J. Toone group