[gmx-users] PULLING

[chris.neale at utoronto.ca]

> 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?

Justin answered this part.

>
> 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...

Here's what I see from a quick scan. I'll also mention that it will  
only take one day to one week to read the manual front to back and it  
will be worth the time.

Note that the snippet you sent did not mention the LJ cutoff. You  
should find out what they used there and modify rvwd.

modify:
;assuming 12 ? means 12 A
rcoulomb            =  1.2
rlist               =  1.2

remove:
define              =  -DFLEXIBLE;

this looks weird:
compressibility     =  13.5e-5
ref_p               =  3.0