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
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
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.
CCG Dept. CFE
Univ. of Milan
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