R: RE: [gmx-users] Concentration

luigi.burgi at virgilio.it luigi.burgi at virgilio.it
Fri Dec 23 11:27:38 CET 2005

I do it too for the counter-ions. In that way the molecules would be 
only randomly subsituted or there is a way to choose where to insert 

The molecule to be subsituted is much bigger than water, in that 
case some other waters in close contact with it would be eliminated?

The best for us would be to have them on the nodes of a grid. (Like 
it's the case when we use genconf.

Thank you,

Da: YGMu at ntu.edu.sg
Data: 23-dic-2005 9.16
A: <luigi.
burgi at virgilio.it>, "Discussion list for GROMACS users"<gmx-
users at gromacs.org>
Ogg: RE: [gmx-users] Concentration

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 
To: gmx-users at gromacs.org
Subject: [gmx-users] Concentration

Gromacs users,
i hope someone can help me out from a little 
have to build a system of a protein in water and a known 
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.
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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