[gmx-users] coupling to water bath

Justin A. Lemkul jalemkul at vt.edu
Sun Dec 16 03:58:37 CET 2007

Quoting pragya chohan <pragyachohan at hotmail.com>:

> 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?

You could do either.  Try make_ndx  -h.  But generally, when I simulate a
protein in water and ions, I simply couple the whole system to the same bath. 
See here:


> I the later case -n option would take in 2 index files. then what should I
> do?

Specify both groups within the same index file.  Again, make_ndx -h.  Type
'help' for some examples.


> Thanks in advance
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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