[gmx-users] Umbrella sampling: window distance - harmonic force constant

[Hermann, Johannes]

Okay. Thanks Justin!


On 27.03.2018 21:12, Justin Lemkul wrote:
>
>
> On 3/27/18 4:44 AM, Hermann, Johannes wrote:
>> Dear All, dear Justin,
>>
>> I am playing around with my umbrella sampling setup and I was looking 
>> at your paper which you linked in your umbrella sampling tutorial 
>> ("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using 
>> Molecular Dynamics").
>> Up to a distance of 2nm you use a 0.1nm spacing, beyond a 0.2nm 
>> spacing. Which harmonic force constant pull_coord1_k do you use for 
>> the 0.1nm spacing? In comparison to the 0.2nm spacing, where 
>> pull_coord1_k=1000.
>> Is there a general rule of thumb between window distance and force 
>> constant? Or is it always try and error while checking the histograms?
>
> You can set the value of k based on experimental methods or somewhat 
> ad hoc, but then yes, you have to check overlap. I don't know of any 
> useful way of trying to predict how the intermolecular forces in the 
> system will respond in such a way that you can exactly say a priori 
> how to set up the windows.
>
> -Justin
>

-- 
______________________________________
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Email: j.hermann at lrz.tum.de
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