> > 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 > reference > >>> (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 > an > >> absolute restraint? Intuitively, the groups should be the bilayer and > the > >> 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 > a > > z-constraining method that involves pulling a single water molecule to > > various z-coordinates (depths in the bilayer), constraining that > molecule, > > 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 > trying > > 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 > defined > >>> center of mass motion removal for the non-waters, which I would expect > to > >>> 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 > spurious > forces due to artificial COM motion. This undercuts your desired approach. > > -Justin >
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 drifting > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
