From: Michael von Domaros (mail_at_vondomaros.eu)
Date: Mon Feb 11 2019 - 18:51:37 CST
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
Can you help me understand these issues?
Thanks a lot!
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:10 CST