[gmx-users] different springs - WHAM

[Erik Marklund]

On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote:

>
>
> On 2/13/13 5:23 PM, Steven Neumann wrote:
>> 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.
>>
>
> The code and/or g_wham paper should address this.  In principle,  
> WHAM can be conducted with any assortment of spring constants you  
> like.  If you track down a bug or something, please report it on  
> redmine.gromacs.org.

I read (and hacked) g_wham not that long ago. If I recall correctly it  
reads the force constants from the tpr. In fact, without those it  
would not be able to use pullf files.

>
> A workaround of course would be to simply add another window (or  
> windows) with the same original force constant that gives adequate  
> sampling.
>
> -Justin
>
> -- 
> ========================================
>
> 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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