[gmx-users] coupling to water bath
Mark.Abraham at anu.edu.au
Sun Dec 16 09:55:30 CET 2007
pragya chohan wrote:
> Dear Users
> I have a system in of protein with in bound chlorine ion. I also added
> Na ion to the system to neutralize charge on system. I have to couple
> the system to water bath. can i couple protein chlorine and Na together
> and solvent separately? or should i couple protein and chlorine together
> and solvent and na together?
Don't use T-coupling groups that might have molecules isolated inside
regions filled by other T-coupling groups. That won't be numerically stable.
> I the later case -n option would take in 2 index files. then what should
> I do?
You can make both groups inside the one index file.
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