[gmx-users] Pulling Mechanics
ahy3nz at virginia.edu
Fri Jan 20 21:36:42 CET 2017
> On 1/16/17 3:04 PM, Alexander Yang wrote:
> > On 1/13/17 6:37 PM, Alexander Yang wrote:
> >>> Hi everyone,
> >>> I am pulling a water molecule into a bilayer using an absolute
> >>> (mdp file below). I have tried to adapt methodology in Justin Lemkul's
> >>> umbrella sampling tutorial, but I have encountered a couple issues:
> >> If you're trying to get water to move into a bilayer, why are you using
> >> absolute restraint? Intuitively, the groups should be the bilayer and
> >> water.
> > My goal is to construct an excess free energy profile of water (in the
> > z-direction) in these bilayer systems to compare permeability. I'm using
> > z-constraining method that involves pulling a single water molecule to
> > various z-coordinates (depths in the bilayer), constraining that
> > and recording the forces on that molecule. My idea has been to use an
> > absolute reference to anchor the water molecule to a particular
> > z-coordinate while still being free to roam in the xy-plane. I'm not
> > to introduce extra forces on the bilayer system itself to pull a water
> > molecule inside.
> >>> 1) The bilayer (already well-equilibrated) is either being pulled or
> >>> drifting. Without the pull code, the bilayer does not move. I've
> >>> center of mass motion removal for the non-waters, which I would expect
> >>> keep the bilayer still. I've copied the mdp file below (Tracer2117
> >>> corresponds to 2117SOL, but I've defined the Tracer2117 group in the
> >> index
> >>> file as the 3 atoms that correspond to this water)
> >> Applying COM motion removal to one group and not another is highly
> >> artificial.
> >> Couple that with your use of an absolute restraint (also somewhat
> >> artificial)
> >> and you're layering bad things upon bad things.
> > Because I was using an absolute reference, I was hoping to keep the
> > equilibrated bilayer still so the profile could be accurately constructed
> > for a profile of z-coordinates.
> But this is not what you will accomplish. You'll get COM resetting in the
> bilayer, then your water will suffer from "flying ice cube" effects and
> forces due to artificial COM motion. This undercuts your desired approach.
I tried the same simulations, but removing water and non-water COM, but
still observed bilayer -drift while pulling with an absolute reference. In
a comparison, removing the entire system's COM also resulted in the bilayer
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