[gmx-users] Regarding calculation of diffusion constant (through MSD) of solvent molecules near protein surface

Apramita Chand apramita.chand at gmail.com
Mon Jan 9 08:32:12 CET 2017

Dear All,
Say I want to calculate how the water molecules near the surface of protein
are diffusing, how would I do that?
Say I look at some hydrogen bonding interactions using VMD and zoom in and
identify the SOL molecules around the surface . Can I create an index file
containing those particular SOL molecules and calculate their diffusion?
Would this work or is there another proper way to do it than just
identifying such solvent molecules visually?



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