From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 11 2019 - 22:15:47 CST
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?
> Are there compelling reasons why one should not use any of these
> thermostats with eABF?
>
> 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?
>
> 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.
>
> Can you help me understand these issues?
>
> Thanks a lot!
>
> Best wishes,
> Michael
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:29 CST