From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 08 2016 - 08:36:45 CST
Hi Sruthi, with that setup it looks like you should be able to compare the
system force integral and log(histogram).
However, you could probably have a very good convergence in the average
force, but a slower convergence in the histogram.
You can see this in an extreme case with only 2 atoms in vacuum, where the
force distribution at fixed distances is infinitely narrow (and obviously
its mean value converges immediately), but the histogram of distances will
take some time before it converges.
On Thu, Jan 7, 2016 at 12:43 PM, sruthi c k <cksruthikvr_at_gmail.com> wrote:
> Hi Giacomo,
>
> Thanks for your reply.
>
> As the hide Jacobian option is NOT activated, I think the system forces
> output includes the Jacobian forces also.If I understand correctly hence
> the free energy surface obtained as -kbT log(histogram) and that by
> integrating <F_system> should match.
>
> Regarding convergence: The average forces look converged when I calculate
> it using data obtained from the 150ns simulation and compare it with
> average forces obtained in 200ns simulation.
>
> Thanks
> Sruthi
>
> On Thu, Jan 7, 2016 at 8:51 PM, sruthi c k <cksruthikvr_at_gmail.com> wrote:
>
>> Dear Sir,
>> I asked about the system forces in the namd mailing list and I am
>> forwarding that mail to you.
>> Thanks
>> Sruthi
>>
>> ---------- Forwarded message ----------
>> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> Date: Thu, Jan 7, 2016 at 8:44 PM
>> Subject: Re: namd-l: Regarding system forces in NAMD
>> To: NAMD list <namd-l_at_ks.uiuc.edu>, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> Cc: sruthi c k <cksruthikvr_at_gmail.com>
>>
>>
>> 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
>>
>>
>>
>>
>
-- 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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