**From:** Matthew Ralph Adendorff (*mraden_at_mit.edu*)

**Date:** Thu Aug 29 2013 - 13:40:42 CDT

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Hi Jerome

Many thanks for the information, it will be highly useful. Might I ask how the value of F is calculated? From the formulation in the NAMD manual it appears to be determined from the running estimate of the free energy gradient at the current point in the collective variable subspace. Therefore, would the value of F be defined at FS/2 from the gradient estimate and then slowly ramped up to F over the n/2 remaining time steps? Or is the target F continually refined? What I am essentially looking for is a way to put an upper bound on the amount of force added per time-step increment to assess the impact this force ramp will have on the slowly relaxing degrees of freedom in the structure, thereby getting a good value for fullSamples in subsequent runs.

Thanks again for the assistance,

Matthew

________________________________________

From: Jérôme Hénin [jerome.henin_at_ibpc.fr]

Sent: 29 August 2013 01:06 PM

To: Matthew Ralph Adendorff

Cc: namd-l_at_ks.uiuc.edu

Subject: Re: namd-l: Linear force ramp increments in ABF

Hi Matthew,

To be precise, the ramp is linear in the number of samples in the bin, and starts at half of fullSamples.

If FS is the value of fullSamples, the current number of samples is n, and the full biasing force is F, the force that is actually applied is:

n < FS/2 : 0

FS/2 < n < FS : (n - FS/2) / (FS/2) * F

n > FS : F

Best,

Jerome

----- Original Message -----

*> Good day,
*

*>
*

*> During an ABF run, I understand that once the minimum number of
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*> samples has been achieved for a given bin the biasing forces are
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*> added following a linear ramp. During this ramp is the force applied
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*> in discrete increments of a fixed value per time-step or does the
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*> applied quantity vary? If so, what is this increment or is there a
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*> procedure to determine how much force is added per step in the
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*> linear ramp?
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*>
*

*> Many thanks for the support.
*

*>
*

*> Best,
*

*>
*

*> Matthew
*

*>
*

*>
*

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