[gmx-users] hybrid solvent model

Leandro Bortot leandro.obt at gmail.com
Tue Jan 8 19:04:35 CET 2013

    I'm also interested in doing this with GROMACS but couldn't find a way
yet. In my case I'm interested in applying it to REMD simulations in which
large conformational changes occur, which makes the implementation more
difficult because the shape of the water layer would be irregular and
change during the simulation.

     Any ideas would help me too.

2013/1/8 Алексей Раевский <rayevsky85 at gmail.com>

> Hi all.
> 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.
> Thank you in advance
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