[gmx-users] different springs - WHAM

Steven Neumann s.neumann08 at gmail.com
Wed Feb 13 23:23:41 CET 2013


On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/12/13 9:57 AM, Steven Neumann wrote:
>>
>> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>>>
>>>>
>>>> Dear Gmx Users,
>>>>
>>>> I know it is possible to combine windows with different spring
>>>> constants into the one PMF curve using g_wham.
>>>>
>>>> Do I have to somehow tell g_wham that one or two windows have
>>>> different spring constants?
>>>>
>>>
>>> No, they are read from the .tpr files.
>>>
>>>
>>>> For instance - I got the better histogram overlap with lower force
>>>> constant in one window. When I replace this window into the window
>>>> with the sring constant like all windwos (worse overlap) both PMF
>>>> curves differ app. 2kcal/mol which is around 30% of the overall
>>>> deltaG.
>>>>
>>>> Is there any error I should inroduce when one window differ in terms of
>>>> k1?
>>>>
>>>
>>> What does g_wham's error analysis suggest?
>>>
>>> -Justin
>>
>>
>> In both PMF error estimate with bayesian bootstraping is app. 0.2 kcal/mol
>>
>
> Seems like a good result, so what's the problem?
>
> -Justin

That the better overlap of histograms produce worse deltaG comparing
to experiment. With all the same spring constants I get the
experimental value of deltaG but there is a poor overlap. There must
be (somehow) a correction added to deltaG when introdcuing windows
with different spring constants.


Steven

>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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