Stéphane Téletchéa wrote:
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.
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.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
