From: sruthi c k (cksruthikvr_at_gmail.com)
Date: Thu Jan 07 2016 - 11:43:49 CST
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
>
>
>
>
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