[gmx-users] seeming paradox with gmx wham
nedomacho at gmail.com
Mon Mar 12 23:54:35 CET 2018
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?
On Mon, Mar 12, 2018 at 4:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/12/18 3:42 PM, Alex wrote:
>> I actually understood your tutorial perfectly well. What I didn't expect
>> is such a significant dependence on direction (assuming spherical symmetry
>> clears the situation).
>> I also had to use direction-periodic instead of distance in your
>> tutorial, because the box is 4 nm wide and grompp is screaming about
>> distance exceeding half-box size. I used 5.0.3 before and it was fine with
>> the 'distance' directive. I think 'direction-periodic' is also wrong for
>> spherical symmetry. So, stick with distance and increase box size?
>> That's the easiest thing to do, yes, as long as the simulation is still
> reasonably efficient.
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
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