[gmx-users] g_spatial Problem

Christopher Neale chris.neale at alum.utoronto.ca
Mon Jan 30 18:54:41 CET 2017

Dear Sakiru:

This topic was discussed before on-list: 

Basically, if you have 48 molecules of A, then you need to process your trajectory so that it is 48x larger in which 48 copies each have a different molecule of A placed first, then all these 48 segments are concatented together and you make the SDF around not the entire A group, but only the first instance of A.

To generate only the SDF of the first shell of B is a little harder and requires either ordering of a fixed number of closest B molecules (different for each frame, but can be done on the 48x trajectory after the procedure noted above).

There is *a lot* of processing before hitting gmx sdf for what you want to do, and perhaps mdanalysis or loos or some other third party anaysis tool can do this out of the box for you — it’s worth checking.

You should also see the noted in an other SDF comment I posted earlier today. Centering with PBC wrapping are going to be important in your preprocessing steps.

To address a couple of your other sub-questions:
- g_spatial does not do fittings, you do them beforehand (which was intended to maximize flexibility of the tool). However, if you have 48 free floating molecules of A and you fit on them and make an SDF of B then you should just be getting random noise, so either (a) pick a single A to fit on and make the SDF of all B (correct, but 48x less data) or use the concatenation procedure above and again fit only on a single molecule of A.
- rotation and translation are intended to be done on the entire system, so both groups plus everything else... this is in the trjconv steps, not g_spatial.
- everything in trjconv or g_spatial is done on all frames unless you use -b -e options to specify not to.


— original message —

                    I want to generate the spatial distribution function of Molecule A around molecules B.

 I have 48 molecules of A and 200 molecules of B in a  cubic box and I want to find the spatial distribution of B around A in the first shell of B ( about 5A away from A based on RDF).
I have followed the steps in the manual and the output does not give a clear picture of what I want to see.
I have a couple of questions:
- Does g_spatial do fittings and analysis on one of the 48 molecules or its averaged?

- How can I select only the region close to molecule A if want to?

- Are the rotation and translation done on both groups as the central molecule was outside the sphere of B generated?

- Is it done on all the frames?
Your help is highly appreciated.

Thank you very much.

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