[gmx-users] Concentration

luigi.burgi at virgilio.it luigi.burgi at virgilio.it
Fri Dec 23 09:00:51 CET 2005

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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