[gmx-users] coupling to water bath

[Mark Abraham]

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.

Mark