[gmx-users] How thick layer of water should one add around aprotein?

Oliver Beckstein oliver at biop.ox.ac.uk
Wed Nov 2 10:51:53 CET 2005

On 2 Nov, 2005, at 08:21, Mu Yuguang (Dr) wrote:

> As a thumb of rule the closest distance between the peptide and the box
> edge > 5 A.
My philosophy is that the water at the edge should have bulk-like 
properties so that you can really pretend to simulate a fully solvated 
protein. Judging from density and diffusion coefficients, SPC water at 
standard conditions becomes bulk-like at a distance of >1 nm from a 
membrane-like slab. Hence I'd choose a water shell of about 1 nm at 
least and check that the water self-diffusion coefficient at the edge 
of your simulation cell is close to the one you get for a pure box of 
SPC (or whatever water model you're using).


> Dr. Yuguang Mu
> Division of Structural and Computational Biology
> School of Biological Sciences
> Nanyang Technological University
> 60 Nanyang Drive
> Singapore 637551
> Tel: 63162885
> Fax: 67913856
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mikko Hellgren
> Sent: Wednesday, November 02, 2005 4:14 PM
> To: gmx-users at gromacs.org; gmx-users at gromacs.org
> Subject: [gmx-users] How thick layer of water should one add around
> aprotein?
> Hi, I have a general question about MD simulations in GROMACS and that
> is how thick water layer that one should add around a peptide. Is there
> some general rules to this. I imagine that this should depend on size
> and the stability of the peptide in a water solution?
> Best regards
> Mikko Hellgren
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Oliver Beckstein * oliver at biop.ox.ac.uk

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