[gmx-users] g_spatial Problem

Badmos, Sakiru sakiru.badmos.14 at ucl.ac.uk
Mon Jan 30 18:37:04 CET 2017

Hi everyone,

                    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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