On 3/12/18 6:54 PM, Alex wrote:
Yeah, enlarging system (4 nm to 6 nm) isn't a problem at this point, it's
still a small system. My sampling pull code is below, I only modified the
bare minimum to work with the new pull code syntax and to enable spherical
slices (radius varying from near-zero to 1.5 nm):

pull                 = yes
pull-coord1-type     = umbrella
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = CL
pull_group2_name        = CNT
pull_coord1_geometry    = distance
pull_coord1_groups      = 1 2
pull_dim                = Y Y Y
pull_coord1_rate        = 0.0
pull_coord1_k           = 1000
pull_start              = yes

CNT is the colloquial name for our membrane. I'm trying to be extra-careful
this time, so I will really appreciate if you see anything else that looks
wrong. Another quick question: it is my understanding that the value of k
will control the histogram width. Is 1000 a reasonable choice overall?

No way to know. It depends on the window spacing and the forces acting in the system. I don't know that anyone has come up with a way to actually know what's "right" for umbrella sampling other than empirical assignment.

Everything else looks reasonable to me.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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