[gmx-users] Position restraints on a lipid bilayer

[Mark Abraham]

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