**From:** wliu (*wliu_at_itcs.ecnu.edu.cn*)

**Date:** Wed Apr 20 2016 - 02:18:01 CDT

**Next message:**Ana Celia Vila Verde: "Re: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Previous message:**Peter Freddolino: "Re:"**Next in thread:**Ana Celia Vila Verde: "Re: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Reply:**Ana Celia Vila Verde: "Re: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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:**Ana Celia Vila Verde: "Re: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Previous message:**Peter Freddolino: "Re:"**Next in thread:**Ana Celia Vila Verde: "Re: How to use a proper force constant to decrease computational cost while keeping calculation precision?"**Reply:**Ana Celia Vila Verde: "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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