From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Sep 01 2010 - 06:11:58 CDT
Dear Carlo,
What you say is correct - the real force constant applied is not the
number you entered but the rescaled version. The simplest thing to do
is check the NAMD output: the colvar module should say exactly what it
does when it rescales the force constant.
About choosing force constants: for US, you want the histograms from
adjacent windows to overlap - either using many narrow potentials, or
fewer broad ones. The role of the potential in SMD is so different
that you can't compare them. The usual theory involves a stiff spring
approximation, so I suppose the constant should be high, whatever that
means.
Cheers,
Jerome
On 31 August 2010 16:45, <guardiani_at_fi.infn.it> wrote:
> Dear all,
>
> I am trying to run umbrella sampling simulations applying an harmonic
> restraint
> to a collective variable corresponding to the distance between two groups of
> atoms. I decided to use a force constant of 15 Kcal/(mol*Ang^2), but reading
> the manual I later realized that the force constant is rescaled by the
> square of the width of the bins of the collective variable. As I am using
> bins of 0.2 Ang, as I understand, the real value of the force constant is
> 15/(0.2)^2 = 375 Kcal/(mol*Ang^2). Now, I am a little confused. Which force
> constant should I enter in the program that performs the WHAM analysis, 15
> or 375 Kcal/(mol*Ang^2) ?
>
> Also, I would like to ask if there is an optimal criterion to choose the
> force
> constant for an umbrella sampling simulation. My goal is to compare the PMF
> generated through umbrella sampling with the PMF computed applying the
> Jarzynski equality to a set of constant velocity SMD simulations ran with a
> force constant of 10 Kcal/(mol*Ang^2). As I understand the force constant
> for
> umbrella sampling should be higher than the one used in standard SMD, but
> how
> much higher ?
>
> Thank you very much for your help ank kind regards,
>
> Carlo Guardiani
>
> PS: I paste here my ColvarsConfig file so you can have a more precise idea
> of
> what I am doing.
>
>
>
> ********************************************************************************
>
> colvarsTrajFrequency 1
> colvarsRestartFrequency 1
>
> colvar {
>
> name COMdistXY
>
> width 0.2
>
> lowerboundary 6.0
> upperboundary 17.0
>
> lowerwallconstant 10.0
> upperwallconstant 10.0
>
> distanceXY {
>
> main {
>
> atomnumbers { 6633 6640 6654 6661 6675 6694 6716 6735 }
>
> }
>
> ref {
>
> atomnumbers { 1681 1703 1719 1730 1742 1763 1778 1795 }
>
> }
>
> axis { (-0.60, 0.26, 0.26) }
>
> }
> ########END OF DISTANCE BLOCK#########################
>
> }
>
> ########END OF COLVAR BLOCK###########################
>
> harmonic {
>
> name umbrella
>
> colvars COMdistXY
>
> centers 6.0
>
> forceConstant 15.0
>
> #################################
> # Only in NAMD 7.2.3
> # targetCenters 15.0
> # targetNumStages 90
> ##################################
>
> targets 17.0
>
> targetsNumsteps 11000000
>
> }
>
> ##########END OF HARMONIC BLOCK#########################
>
> histogram {
>
> colvars COMdistXY
>
> outputFreq 1
>
> }
>
> ##########END OF HISTOGRAM BLOCK#########################
>
>
>
>
>
>
>
>
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