Re: CSVR + eABF, system temperature set to zero

From: Michael von Domaros (mail_at_vondomaros.eu)
Date: Tue Feb 12 2019 - 16:38:01 CST

Dear Giacomo and Jerome,

thanks for your prompt replies. I didn't realize the NAMD proxy is being
maintained as part of the colvars project. I created a pull request with
the fix on github.
The other issue seems indeed be related to improper concatenation.

Best wishes,
Michael

On Tue, Feb 12, 2019 at 5:54 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Sorry, I missed CSVR because it's not named that way in the NAMD user's
> guide.
>
> Lowe-Andersen is statistically correct.
>
> Jerome
>
>
> On Tue, 12 Feb 2019 at 14:20, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>>
>>
>> On Tue, Feb 12, 2019 at 8:10 AM Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> wrote:
>>
>>> Dear Michael,
>>>
>>>
>>> On Tue, 12 Feb 2019 at 05:18, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>>> wrote:
>>>
>>>> This is not a bug, but to paraphrase a major software house, "it's a
>>>> (lack of) a feature" :-) NAMD does not have a general method to provide
>>>> the ensemble's target temperature, but it can be given one, so that these
>>>> cases are all considered.
>>>>
>>>> If you would like, you can modify the code yourself with your patch for
>>>> everybody's benefit at https://github.com/Colvars/colvars.
>>>>
>>>> I'll let others comment on the role of the temperature in the various
>>>> estimators, but seeing as kT appears at the denominator of many quantities
>>>> the derivation of any sampling method is flawed for T=0.
>>>>
>>>> Giacomo
>>>>
>>>> On Mon, Feb 11, 2019, 7:53 PM Michael von Domaros <mail_at_vondomaros.eu
>>>> wrote:
>>>>
>>>>> Dear NAMD users,
>>>>>
>>>>> I'm trying to run meta-eABF in combination with the CSVR thermostat.
>>>>> When doing so, I get the error message "WARNING: ABF should not be run
>>>>> without a thermostat or at 0 Kelvin!".
>>>>>
>>>>> This appears to be the case, because the function cvm::temperature()
>>>>> returns 0.0 K for CSVR, which is because CSVR is not included in
>>>>> colvarproxy_namd.C. After I added the corresponding if statement, the
>>>>> warning went away. Is this a bug?
>>>>> Related question: Why is loweAnderson commented out at the same place?
>>>>>
>>>>
>>> I'm not sure. It's been that way ever since that code was written,
>>> apparently. I don't see a reason not to enable it.
>>>
>>>
>>>> Are there compelling reasons why one should not use any of these
>>>>> thermostats with eABF?
>>>>>
>>>>
>>> Velocity rescaling does not generate a correct statistical ensemble, and
>>> I don't know of a good reason to use it for anything at all, really.
>>>
>>
>> This is probably true about Lowe-Andersen, but Bussi's CSVR thermostat
>> should probably be accounted for.
>>
>>
>>
>>>
>>>
>>>> Second problem: As far as I understand the code, cvm::temperature() is
>>>>> also used in the calculation of the CZAR gradients in
>>>>> colvarbias_abf::write_gradient_samples(). A system temperature of zero
>>>>> would make the kT ln(rho(z)) term of the czar estimator zero, so results
>>>>> would be wrong. Is this correct?
>>>>>
>>>>
>>> That is correct. Neither CZAR, nor ABF, nor free energy in general makes
>>> much sense at T=0K.
>>>
>>>
>>>> I'm asking, because a co-worker is doing meta-eABF with CSVR in NAMD
>>>>> and her PMF's converge to those obtained through ABF with a langevin
>>>>> thermostat, despite of these issues above. When I asked her to do a 0
>>>>> length run with langevin on, which should rewrite the CZAR files with the
>>>>> correct temperature, she observed discontinuities in her PMF at the window
>>>>> boundaries.
>>>>>
>>>>
>>> That may also involve a separate issue, which is that CZAR is defined
>>> based on sampling in a contiguous window. Stitching together separate
>>> windows will produce artefacts. The correct way to combine those windows is
>>> to run CZAR in each window individually, and then merge the resulting free
>>> energy gradients "by hand", and integrate them. I still need to clarify
>>> this in the documentation.
>>>
>>> Best,
>>> Jerome
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>

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