Potential of mean force calculation using colvars in NADM 2.9 package

From: 辑侩老 (seoyi86_at_gmail.com)
Date: Thu May 16 2013 - 02:06:53 CDT

Dear NAMD users

We perform MD simultaions for potential of mean forece calculation using
colvars module in NAMD_2.9_Linux-x86_64-multicore package.

The system is one potassium ion in 2135 waters on NVT esemble (V = 40.0 x
40.0 x 40.0 A^3, T = 298.15 K).

Colvars parameters are below:

colvarsTrajFrequency 2

colvar {

name ProjectionXY_ion

width 2.5

distanceXY {

main {

atomNumbersRange { 1-1 }

}

ref {

dummyAtom ( 0.0, 0.0, 0.0 )

}

axis (0.0, 0.0, 1.0)

}

}

colvar {
name ProjectionZ_ion

width 0.4

lowerboundary -15.0
upperboundary 15.0

lowerwallconstant 10.0
upperwallconstant 10.0

distanceZ {
main {
atomNumbersRange { 1-1 }
}
ref {
dummyAtom ( 0.0, 0.0, 0.0 )
}
axis (0.0, 0.0, 1.0)
}
}

harmonic {
colvars ProjectionXY_ion
forceConstant 1.0
centers 0.0
}

harmonic {
colvars ProjectionZ_ion
forceConstant 1.0
centers -10.0
targetCenters 10.0
targetNumSteps 100000
targetNumStages 50
}

Later simulations, i calculate potentail of mean forece using umbrella
sampling with WHAM.

We expect that the free energy is changed little.

But, The defference of free enegy between the initial window and final
window is 25.336992 to target centers from centers.

So, I performed the same simulations using namd2.8_64-multicore with the
same module and parameter sets.

In this case, the difference of free energy is 0.095781.

Link to the PMF
profiles<http://4.bp.blogspot.com/-qJnJclWf6uw/UYmxTjftt6I/AAAAAAAAAAc/5cUXbWe1s6s/s1600/pmf.png>

I'm wondering why there is some differences between NAMD 2.8 and 2.9?
Do i need to add other options or paramters about this colvars in 2.9
package?

Yongil Seo

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