**From:** Ana Celia Vila Verde (*acavilaverde_at_gmail.com*)

**Date:** Wed Apr 20 2016 - 03:03:08 CDT

**Next message:**giulia palermo: "rotation angle"**Previous message:**wliu: "How to use a proper force constant to decrease computational cost while keeping calculation precision?"**In reply to:**wliu: "How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Next in thread:**Radak, Brian K: "RE: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Reply:**Radak, Brian K: "RE: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Wei,

The article by Roux, B., The calculation of the potential of mean force

using computer simulations

/Computer Physics Communications, /*1995*/, 91/, 275-282

is very useful.

In general, running more windows with a slightly larger k is more

efficient than running fewer windows with lower k. Keep in mind that

there is no single value of k which is correct; many values of k,

coupled with different numbers of windows, will give you a good result,

provided that all windows overlap. Your k=35 might work with windows

that are 5, or even 10 degrees apart, for example. If you want to test,

and given that your system does not appear to be very complicated, you

can do a couple of other runs where you take the same k but use smaller

and larger windows, and see how your PMF is affected. If you reach a

point where two runs with different window sizes give the same PMF,

despite different overlap between windows, then you know you have enough

sampling.

Oh, you should always use WHAM to build your PMF from umbrella sampling...

I hope it helps,

Ana

On 20/04/16 09:18, wliu wrote:

*> Dear all,
*

*>
*

*> Recently, I am learning how to use umbrella sampling method to
*

*> calculate the potential mean force of one torsion angle of a specific
*

*> residue in a protein. I am curious about how to choose the force
*

*> constant wisely.
*

*>
*

*> If k is too large, to fulfill the overlap, we have to employ more
*

*> windows. On the contrary, the center value of torsion we set will be
*

*> displaced largely. So, is there any quantitative criterion to judge if
*

*> the value of k is reasonable (small enough and can guarantee the PMF
*

*> calculation precision)?
*

*>
*

*> For example, if we set k=35, χ0=110, after a short time's MD (such as
*

*> 6 ns), I got the distribution of χ, then I calculation the mean of χ,
*

*> <χ>=104.12, standard deviation σχ=6.04. Then the displacement Δχ=5.88
*

*> (<σχ). Thus, we consider k=35 to be confident (within 68% of Gaussian).
*

*>
*

*> Any suggestions or relevant literatures will be appreciated.
*

*>
*

*> Wei
*

*>
*

**Next message:**giulia palermo: "rotation angle"**Previous message:**wliu: "How to use a proper force constant to decrease computational cost while keeping calculation precision?"**In reply to:**wliu: "How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Next in thread:**Radak, Brian K: "RE: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Reply:**Radak, Brian K: "RE: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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