[gmx-users] seeming paradox with gmx wham

[Justin Lemkul]

r

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

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

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