[gmx-users] how to indicate solvent flexibility?

Albert mailmd2011 at gmail.com
Tue Jan 8 17:42:43 CET 2013


   I've finished a 60ns MD simulation with Gromacs and I found that the 
flixbility of solvent molecules inside the protein is different when it 
binds with different ligands: ie. in one case the solvent can move very 
fast with bulk environment, and in other case the solvent forms type 
Hbonds with resdiues inside protein.  I am just wondering how which 
module of Gromacs can I use to indicate the solvent difference in 
flexibility? Is it possible to calculate the entropy in certain region 
(let's say: 20<Z<30 ) of the solvent?

thank you very much

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