[gmx-users] different springs - WHAM

[Steven Neumann]

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

>
>
>> The deltaG value of my PMF with all the same windows (springs) is the
>> exact experimental value but has worse overlap.
>>
>> Can you advise?
>>
>> 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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