[gmx-users] Free energy calculations and distance restraints

[Matteo Aldeghi]

Dear users,

I would like to apply a particular set of harmonic restraints (1 distance, 2
angles, 3 dihedrals) between a ligand and a protein. This is for free energy
calculations so I would like them to be lambda-dependent.

>From the manual of Gromacs 4.6.3 (page 210) I understand that in
'restraint-lambdas' "Only the restraint interactions: dihedral restraints,
and the pull code restraints are controlled with this component of the
lambda vector." Also, in Table 5.5 (page 133) I notice that (contrary to
angle_restraints and dihedral_restraints) distance_restraints does not have
any information under the column "Use in F.E.?".

1. I thus wonder if it's not possible to use distance restraints with the
free energy features in gromacs, or this is simply not reported in the
manual and restraint-lambdas would in fact control this too just like it
does for angles and dihedrals.

2. If it is actually not possible to use distance_restraints with the free
energy options, what would be the best (or possible) alternative to obtain
lambda-dependent harmonic distance restraints? Can the pull code be used to
give the same result?

Many thanks,

Matteo

PS.1. these might be trivial questions but I am new to gromacs and free
energy calculations and I could not find specific information on this.
PS.2. I know the restraints require ligand and protein to be a single
moleculetype, which does not go well with the fact "couple-moltype" requires
the opposite. I have noticed the issue has already been raised and there is
a patch that might deal with this:
https://gerrit.gromacs.org/#/c/2566/


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