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.
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.
-Justin
2) I'm getting an error that the distance between the pull groups is larger than 0.49 times the box size (the box is about 6.12 nm x 5.17 nm x 7.42 nm). The origin of my absolute reference is only 0.1 nm away from the water molecule. The way I've specified my pull-coord-rate, at the timestep when the pull distance is larger than half the box size, the distance between the origin of the reference at time 0 and the water molecule at time of crash exceeds half the box size. Is the reference position actually moving, or does the pull-coord-rate specify a change to a quantity besides the reference position such that the water molecule can be pulled while the reference position stays where it originally was specified? @ time 0 ns: Water (3.794, 1.447, 1.150), reference origin (3.794, 1.447, 1.250) @ crash (time 47.19ns): Water(3.997, 0.032, 4.751). My pull-coord-rate is 7.7e-5 nm/ps, so would the reference be at (3.794, 1.447, 4.883)? If this is the case, I'm not sure how this distance violates the box size rule. However, the distance between reference @ t=0 and water @ t = 47.19ns, violates the 0.49 box size rule. ******* Mdp File *********** Run MDP parameters integrator = md dt = 0.002 nsteps = 25000000 comm-mode = Linear nstcomm = 1 comm-grps = non-water ; Output parameters nstxout = 0 nstvout = 0 nstxtcout = 5000 nstenergy = 5000 nstlog = 5000 nstfout = 0 ; Bond parameters continuation = yes constraint-algorithm = lincs constraints = all-bonds lincs-iter = 1 lincs-order = 4 ; Neighbor searching cutoff-scheme = Verlet nstlist = 10 rcoulomb = 1.4 rvdw = 1.4 ; Electrostatics coulombtype = PME fourierspacing = 0.16 pme_order = 4 ; Temperature coupling tcoupl = nose-hoover tc_grps = non-water water tau_t = 0.4 0.4 ref_t = 305 305 ; Pressure coupling pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-05 refcoord_scaling = com ; Misc stuff gen_vel = no pbc = xyz DispCorr = EnerPres ; Pull parameters pull = yes pull-nstxout = 5000 pull-nstfout = 5000 pull-ngroups = 1 pull-ncoords = 1 pull-group1-name = Tracer2117 pull-coord1-groups = 0 1 pull-coord1-type = umbrella pull-coord1-geometry = direction pull-coord1-origin = 3.794 1.447 1.250 pull-coord1-dim = N N Y pull-coord1-rate = 7.7e-05 pull-coord1-vec = 0 0 1 pull-coord1-k = 500.0 pull-coord1-start = no ************* I've attached URLS to snapshots below (time0 and time47). Red is water, grey is the lipid bilayer, yellow is the water molecule (enlarged for visibility), and I've placed axes in the center. Before the crash, the water molecule was definitely moving in the correct direction (positive z). The bilayer drifted in the direction the water molecule was moving. (time0) http://imgur.com/a/jWu33 (time47) http://imgur.com/a/nekmL Thanks for the help, Alex
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
