[gmx-users] Pulling Mechanics

[Alexander Yang]

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:

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)

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