[gmx-users] seeming paradox with gmx wham

[Justin Lemkul]

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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-- 
==================================================

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

==================================================