[gmx-users] different springs - WHAM

[Justin Lemkul]

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

-- 
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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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