[gmx-users] Counting particles in a particular region

[xi zhao]

I want to calculate the number of water between protein and ligand in entire simulation process , I can not  konw if your program is suitable for this question. Thank you!

Oliver Beckstein <oliver at biop.ox.ac.uk> 写道:> Dear sir : I am GMX user . I need your tool "g_occupancy"to calculate
> water number in certain region. Thank you in advance!

I'm not entirely sure what you want to count, and in which region, but you
could try some of the following:

- ask David Bostick for g_occupancy.c (or perhaps he had already posted
the code here or on the contributions page?)

- trjorder

- try to compile my g_count
http://sansom.biop.ox.ac.uk/oliver/download/Gromacs/g_count-0.1.tar.bz2
(less general than g_occupancy)

- try to compile my gridcounter (for 3D densities, see
http://sansom.biop.ox.ac.uk/oliver/software/#gridcount )

(Please take note of the remarks in
http://sansom.biop.ox.ac.uk/oliver/download/Gromacs/ with respect to
disclaimers, licensing, compiling and reporting bugs)

Oliver

--
Oliver Beckstein * oliver at biop.ox.ac.uk
http://sansom.biop.ox.ac.uk/oliver/

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