Dear all, I apologize for having sent four identical messages! Since I
didn't get my message back (as it always happened), I thought there
were some problems with the client, or that I had been banned for some
reason..Sorry again, and thanks for the very detailed answer. I will
try your suggestions, and I will let you know.
Many thanks
Lorenzo
2011/9/22 Thomas Cheatham III <tec3.utah.edu>:
>
>> 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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>
--
=======================================
Lorenzo Gontrani
Research associate of EDXD group
University of Rome "La Sapienza"
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it
Webpage: http://webcaminiti/gontrani.html
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Received on Thu Sep 22 2011 - 23:00:02 PDT
