**From:** Jérôme Hénin (*jhenin_at_ifr88.cnrs-mrs.fr*)

**Date:** Wed Sep 01 2010 - 06:11:58 CDT

**Next message:**ehenriques_at_qui.uc.pt: "Re: Building PSF file for protein with ions"**Previous message:**anas .: "Building PSF file for protein with ions"**In reply to:**guardiani_at_fi.infn.it: "Force constant scaling"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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,
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*>
*

*> I am trying to run umbrella sampling simulations applying an harmonic
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*> restraint
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*> to a collective variable corresponding to the distance between two groups of
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*> atoms. I decided to use a force constant of 15 Kcal/(mol*Ang^2), but reading
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*> the manual I later realized that the force constant is rescaled by the
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*> square of the width of the bins of the collective variable. As I am using
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*> bins of 0.2 Ang, as I understand, the real value of the force constant is
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*> 15/(0.2)^2 = 375 Kcal/(mol*Ang^2). Now, I am a little confused. Which force
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*> constant should I enter in the program that performs the WHAM analysis, 15
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*> or 375 Kcal/(mol*Ang^2) ?
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*>
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*> Also, I would like to ask if there is an optimal criterion to choose the
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*> force
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*> constant for an umbrella sampling simulation. My goal is to compare the PMF
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*> generated through umbrella sampling with the PMF computed applying the
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*> Jarzynski equality to a set of constant velocity SMD simulations ran with a
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*> force constant of 10 Kcal/(mol*Ang^2). As I understand the force constant
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*> for
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*> umbrella sampling should be higher than the one used in standard SMD, but
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*> how
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*> much higher ?
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*>
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*> Thank you very much for your help ank kind regards,
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*>
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*> Carlo Guardiani
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*>
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*> PS: I paste here my ColvarsConfig file so you can have a more precise idea
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*> of
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*> what I am doing.
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*>
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*>
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*>
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*> ********************************************************************************
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*>
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*> colvarsTrajFrequency 1
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*> colvarsRestartFrequency 1
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*>
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*> colvar {
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*>
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*> name COMdistXY
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*>
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*> width 0.2
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*>
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*> lowerboundary 6.0
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*> upperboundary 17.0
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*>
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*> lowerwallconstant 10.0
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*> upperwallconstant 10.0
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*>
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*> distanceXY {
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*>
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*> main {
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*>
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*> atomnumbers { 6633 6640 6654 6661 6675 6694 6716 6735 }
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*>
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*> }
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*>
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*> ref {
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*>
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*> atomnumbers { 1681 1703 1719 1730 1742 1763 1778 1795 }
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*>
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*> }
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*>
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*> axis { (-0.60, 0.26, 0.26) }
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*>
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*> }
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*> ########END OF DISTANCE BLOCK#########################
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*>
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*> }
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*>
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*> ########END OF COLVAR BLOCK###########################
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*>
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*> harmonic {
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*>
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*> name umbrella
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*>
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*> colvars COMdistXY
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*>
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*> centers 6.0
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*>
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*> forceConstant 15.0
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*>
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*> #################################
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*> # Only in NAMD 7.2.3
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*> # targetCenters 15.0
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*> # targetNumStages 90
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*> ##################################
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*>
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*> targets 17.0
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*>
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*> targetsNumsteps 11000000
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*>
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*> }
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*>
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*> ##########END OF HARMONIC BLOCK#########################
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*>
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*> histogram {
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*>
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*> colvars COMdistXY
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*>
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*> outputFreq 1
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*>
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*> }
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*>
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*> ##########END OF HISTOGRAM BLOCK#########################
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*>
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*>
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*>
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*>
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*>
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*>
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*>
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*>
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