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

[Ran Friedman]

In addition to Oliver's comment, I'd say it's also a matter of the 
structural changes during the simulations: if the structure of the 
peptide becomes more extended, then it may become closer to the edge of 
the box during the simulation.

Ran.

Oliver Beckstein wrote:

> 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).
>
> Oliver
>
>> 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
>     http://sansom.biop.ox.ac.uk/oliver/
>
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-- 
------------------------------------------------------
Ran Friedman
http://bioinfo.tau.ac.il/~ran
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
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