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

**Date:** Thu Aug 29 2013 - 14:56:30 CDT

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Hi Jerome

I will definitely have a look at the code. In contrast, would the Metadynamics method follow a more uniform (dare I say more trivial) addition of force to the system in the form of controlling the hillWeight and hillWidth variables?

Best,

Matthew

________________________________________

From: Jérôme Hénin [jerome.henin_at_ibpc.fr]

Sent: 29 August 2013 03:15 PM

To: Matthew Ralph Adendorff

Cc: namd-l_at_ks.uiuc.edu

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

Hi Matthew,

If you are into coding, the calculations are done in the file colvarbias_abf.C - look for the variables full_samples and min_samples. What happens to the biasing force over time is non-trivial, as the coordinate may move between bins at the same time as the value of the multiplying factor changes in each bin.

Cheers,

Jerome

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

*> 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
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*> NAMD manual it appears to be determined from the running estimate of
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*> the free energy gradient at the current point in the collective
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*> variable subspace. Therefore, would the value of F be defined at
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*> 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
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*> refined? What I am essentially looking for is a way to put an upper
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*> bound on the amount of force added per time-step increment to assess
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*> the impact this force ramp will have on the slowly relaxing degrees
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*> of freedom in the structure, thereby getting a good value for
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*> 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
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*> 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
*

*> > samples has been achieved for a given bin the biasing forces are
*

*> > added following a linear ramp. During this ramp is the force
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*> > applied
*

*> > 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?
*

*> >
*

*> > Many thanks for the support.
*

*> >
*

*> > Best,
*

*> >
*

*> > Matthew
*

*> >
*

*> >
*

*>
*

**Next message:**Kenno Vanommeslaeghe: "Re: problem in determining atom types and charges for ligand atoms to type in the topology file"**Previous message:**JÃ©rÃ´me HÃ©nin: "Re: Linear force ramp increments in ABF"**In reply to:**JÃ©rÃ´me HÃ©nin: "Re: Linear force ramp increments in ABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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