[gmx-users] PULLING

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 16 12:42:53 CET 2009

Алексей Раевский wrote:
> Sorry for so disordered questions...
> <3. use the pull code. I don't know exactly what you want to do 
> here...perhaps harmonically restrain the distance between the two 
> mentioned groups to some specified value? No need to rename the water, 
> just make an index group.>
> The problem is that I don't know how to create index group (like 
> "protein" or "non-protein"), cause I have to unite H2O (the most close 
> to the carbonyl carbon) and the carbonyl carbon of valyn, just an atom 
> not full residue. So I don't understand how to identify this atom for 
> gromacs...by number of atom in whole structure or something else?

Please see the make_ndx documentation.  Conveniently, there are even a few 
examples on the Gromacs site:


You can also type "h" at the make_ndx prompt for even more examples of how to 
use this program.


> P.S. about the list of functions in mdp I sent you, I wanted to be sure 
> I have chosen everything I had to...according to the article...
> Thank you very much, sory for disturb.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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