[gmx-users] Using the Pull Code to Restrain Ice

Daniel Kozuch dkozuch at princeton.edu
Sun Sep 10 16:37:54 CEST 2017


I am attempting to restrain an ice sheet in a system with liquid water. I
initially considered using position restraints, but it seems like GROMACS
has a few quirks that make that difficult: you have to create a new .itp
and define the crystal water as different from the liquid water and then
use constraints instead of settle, etc.

I was hoping that the pull code might be an easier alternative by using the
initial coordinates as reference coordinates (pull-coord1-groups= 0 1) and
pull-geometry=distance. This has the added bonus of the pull code allowing
for slow tuning of the force constant (via the free energy code) which I
would like to use.

However, this of course gives lots of warnings about using absolute
reference coordinates and artifacts from translation/rotation. Is there a
good way to go about doing this?

I know ideally the pull code would use some other part of the system as a
reference, but I would like to keep pressure coupling and I cannot do that
with a reference molecule since I would need to use
pull-geometry=direction-periodic which does not allow for changes in the
box size.

Any suggestions are welcome.


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