[gmx-users] Position restraints on a lipid bilayer

[Stéphane Téletchéa]

toma0052 a écrit :
> Hello,
>      I am looking to add position restraints to some atoms of a lipid
> bilayer.  There seem to be a lot in the list archives on this subject, but I
> am still a tad confused.  What I would like to do is to position restrain the
> phosphorus atoms in only one leaflet of the bilayer.  So how do I generate
> such a pr file, and where should I include it?  It seems as if things are
> done per molecule, so if I put it in my *.top or *.itp files, the restraint
> is on all P atoms in the system, not just the ones I want.  Is there a way to
> do this so that things are indexed per atom rather than per molecule?
> 
> Thanks,
> Mike
> 

In order to constrain only the P of lipids, i usually create an index 
like this:

make_ndx \
       -f input.gro \
       -o out &> lipid_posre_index.log <<EOF
"DPPC" & a P
q
EOF

Where "DPPC" is the lipid atom name, and "a P" indicates i'm selecting 
the atom P, the command will create a new group named DPPC_&_P.

Then, you use the positional restraint in you mdp file and in the 
"Constraints" section, i use:

freezegrps               = DPPC_&_P
freezedim                = N N Y

The N N Y indicates i'm not constraining on x, not cnostraining on y, 
and just constraining in z.

Yours,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901