[gmx-users] Position restraints on a lipid bilayer
Mark.Abraham at anu.edu.au
Mon Mar 10 18:42:32 CET 2008
Stéphane Téletchéa wrote:
> toma0052 a écrit :
>> 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
>> 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
>> 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?
> 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
> 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.
That approach can achieve a similar effect in some situations, but there
are caveats in manual sections 3.3 and 7.3.21 that should be noted.
Additionally, selecting P atoms in only one leaf of the bilayer will
require more work than the above.
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