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

[Mu Yuguang (Dr)]

As a thumb of rule the closest distance between the peptide and the box
edge > 5 A. 

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