Hi, dear users and developers!
I need your help. I'm working with both packages amber/gromacs and I have a
goal to investigate nucleophilic substution.
I want to create a system with hybrid solvent (explicit/implicit). My
system is large enough to calculate it with explicit SOL. But it is
critical to study the behavior of several water molecules in the site. The
idea is to generate a layer of explicit water molecules around the protein
molecule with ligand in the binding site and than fill the box with
continuous imlicit solvent with epsilon = 80. It will reduce a
computational time. To prevent the departure of discrete water molecules
into the implicit layer I want to limit the distance of their movement with
something like distance constraints or anything else. Is it real or I have
to find another way or choose another software for this purpose.
Thank you
--
*
Nemo me impune lacessit*
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Received on Wed Jan 09 2013 - 03:00:02 PST
