[gmx-users] seeming paradox with gmx wham

[Alex]

You actually pointed this symmetry situation out when I was calculating
something that's already been submitted, so the gratitude is all mine.
Hopefully, it doesn't produce much of a difference in that particular case,
but I really should have listened. The path to correcting possible
artifacts is clear. :)

Alex

On Mon, Mar 12, 2018 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/12/18 6:59 PM, Alex wrote:
>
>> Great, thanks. I believe this necessitates an acknowledgment. You go by J.
>> A. Lemkul in your papers, correct?
>>
> That would work. Much obliged :)
>
> -Justin
>
>
> On Mon, Mar 12, 2018 at 4:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
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>>>
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> --
> ==================================================
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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> Gromacs Users mailing list
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