[gmx-users] Concentration

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Fri Dec 23 09:16:33 CET 2005

Could you first solvate that protein with pure water. And then replace
the solvating water molecules with other molecules you want to add.
In DNA simulation we do this way to add counter ions.

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
luigi.burgi at virgilio.it
Sent: Friday, December 23, 2005 4:01 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Concentration

Dear Gromacs users,
i hope someone can help me out from a little 
I have to build a system of a protein in water and a known 
concentration of other molecules.
I tried to build and equilibrate a 
small box of solvent at the right concentration, but when i solvate the 
protein the ratio water/other molecules changes.
I think that this 
happens because of the removal of molecules with close contacts with 
the protein.
I could arrive at the wanted conc. by trial and error but 
that would cost very much time. (many different molecules and different 
Anyone can suggest me a way to overcome this problem. 
Thank you,
Luigi Burgi

CCG Dept. CFE 
Univ. of Milan

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