[gmx-users] repost_hybrid imlicit/explicit solvent

Justin Lemkul jalemkul at vt.edu
Wed Jan 9 14:51:41 CET 2013

On 1/9/13 6:02 AM, Алексей Раевский wrote:
> Hi this is a repost, maybe it was missed.
> 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. To prevent the departure of
> discrete water molecules into the implicit layer I want to limit the
> distance of their movement with something like PULL COM distance or
> anything else. Is it real or I have to find another way or choose another
> software for this purpose.

Perhaps something like a spherical restraint would be more useful than the pull 
code, as was done in http://www.pnas.org/content/108/17/6838.  The spherical 
restraint potential has been implemented in the master development branch, and 
thus won't appear in the next release (4.6) but perhaps you can easily patch the 
source to use this feature.  I have no idea how that will play with an external 
implicit environment, but it's probably worth a shot.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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