[gmx-users] pull code questions

[David Mobley]

Dear all,

I had a couple quick questions on the pull code, as I couldn't quite
figure this out from the documentation. In particular, I'm interested
in the part that does umbrella sampling:

1) If an alternative reference structure is provided to grompp using
the -r option (as one would do for position restraints), is this
structure used for the reference atom positions for the reference
group, or are these positions always taken from the input coordinate
file (grompp -c)?
2) I am a bit nervous about umbrella sampling simply the distance
between (in this case) a protein and the ligand, as convergence times
will grow quite long as the distance increases since the ligand has to
sample a larger and larger spherical shell around the reference group.
I would prefer to umbrella sample along some particular direction (but
not simply the X, Y, or Z axis). Is there an easy way to do this with
the existing pull code?

Thanks,
David