[gmx-users] seeming paradox with gmx wham
nedomacho at gmail.com
Mon Mar 12 23:59:35 CET 2018
Great, thanks. I believe this necessitates an acknowledgment. You go by J.
A. Lemkul in your papers, correct?
On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> jalemkul at vt.edu | (540) 231-3129
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