From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jan 07 2016 - 09:14:45 CST
Sorry, one clarification: I meant to say that the Jacobian force is not
calculated *explicitly* within the histogram, but it is implicitly included
in it and the histogram carries full thermodynamic information (at least
for that variable).
Giacomo
On Thu, Jan 7, 2016 at 10:10 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi, a small addition about the comparison with the histogram. The
> Jacobian force (which is very strong near zero for many distance-related
> variables as Jérôme said) is only calculated explicitly for system forces,
> but is not implemented for histograms.
>
> You can either:
> 1) use the hideJacobian option of ABF (and you must use ABF with
> "applyBias off" to calculate the system-force profile); or
> 2) add instead the Jacobian force to the derivative of the histogram,
> using the formula for that specific colvar, as listed in the tables of our
> reference paper.
>
> Lastly, note that until full convergence is achieved, it is perfectly
> normal to have different PMFs from the system force vs the histogram.
>
> Giacomo
>
> On Thu, Jan 7, 2016 at 9:37 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi Sruthi,
>>
>> If you are looking at a radius of gyration, keep in mind that that
>> coordinate experiences a strong Jacobian force especially at small values.
>> Essentially, entropy tends to pull the particles apart, while cohesive
>> forces from the force field keep it together - those would be almost always
>> negative. Did you activate the hideJacobian option?
>>
>> Jerome
>>
>> On 7 January 2016 at 13:49, sruthi c k <cksruthikvr_at_gmail.com> wrote:
>>
>>> Dear NAMD developers,
>>>
>>> I have some queries about the system forces that are calculated in the
>>> COLVAR module implemented in NAMD.
>>>
>>> I was trying to generate the free-energy surface by integrating the
>>> <F_system> on the colvar obtained from an unconstrained and unbiased MD
>>> simulation.
>>>
>>> I did 200 ns equilibrium molecular dynamics (NPT) simulation (NO BIAS
>>> APPLIED) and collected the system force acting on the colvar. The
>>> <F_system> for a given bin of the colvar was then calculated by taking the
>>> average of the system forces corresponding to the rg values falling in that
>>> bin.
>>>
>>> What I observe is that <F_system> is a straight-line but it is all
>>> negative numbers. I was expecting that <F_system> will be equal to zero
>>> where the histogram of colvar has a peak and +ve and -ve on either side of
>>> it.
>>>
>>> Could you please help me in understanding this?
>>> Thanks in advance
>>>
>>> Regards
>>> Sruthi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html
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