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Re: [lammps-users] Umbrella Sampling/ PMF
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Re: [lammps-users] Umbrella Sampling/ PMF


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 20 Dec 2017 11:32:06 -0500



On Wed, Dec 20, 2017 at 11:07 AM, Robert McAllen <mm229196@...1064...278...> wrote:

Thanks, Axel.

But, I've already searched web thoroughly. All discussions are short and vague.

​if they are too short and too vague for you, you have to get a text book.​ there should be introductions in any text book on MD that is worth having. if that is not sufficient, you can look at chris chipot's book and/or the many, many articles published on various methods and review articles comparing methods or benchmarking methods for managing statistical errors.
 

I'm seeking for anything like a lecture or movie, suitable for simply learning concept of PMF and Umbrella Sampling

the basic concepts of a PMF or Umbrella sampling *are* quite simple.

concept 1) since you get a force​ as the derivative of the potential, it is just logical, that integrating the force with respect to a given coordinate will give you a potential.
concept 2) to improve sampling across the selected coordinate (or collective variable) you apply a biasing force, e.g. a position restraint

​there isn't really much to it unless you are lacking a require understanding of statistical mechanics fundamentals.

besides. in my experience online media like recorded lectures and ​alike are rarely effective. working your way through examples and reproducing results and then modifying them and understanding the changes in results is the most effective way to learn and understand. there is no replacement for getting your hands dirty, making mistakes, learning from them and consulting (in person) with experienced colleagues.

​axel.​

 



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On Wed, Dec 20, 2017 at 7:09 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Wed, Dec 20, 2017 at 10:13 AM, Robert McAllen <mm229196@...7278...> wrote:
Dear users

Could anybody introduce an illustrative text for concept of
Umbrella Sampling and Potential of Mean Force

What is the physical meaning underlying those?
How are they calculated? 

​i think this is a discussion that you should have with your adviser/supervisor.

...and if you've been a nice person, you might ask santa's little helpers to have him stuff something like this into your stockings: http://www.springer.com/us/book/9783540384472

​axel.​


 

Bests




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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.




--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.