From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Feb 25 2013 - 07:07:39 CST
This next questions is similar to asking "I poured kerosene into my car --
why did it explode?". But bear with me for the next paragraph, perhaps it
is not so bad.
I performed 400 ns of ABF simulations on the phi and psi angles of the
alanine dipeptide in vacuum.
Then I made a short run without using the thermostat. This was done on
purpose and I did of course notice the warning printed by the colvars
module. The net result of this was that my system heated up considerably.
I realize that meta-dynamics always puts energy into the system, but I had
the feeling that since ABF is a time dependant potential it could input
energy in some bins and output energy in other, so that the net work done
on the system would be small. So my questions are:
- *Does ABF always pump energy into a system and what factors determine
if energy goes in or out? *
- *What thermostat is the most suitable for ABF? *(Langevin, tCouple,
Probably the best thermostat is the one that does not hinder diffusion
too much, so the answer would be Lowe-Andersen, but that does not work with
CUDA, so the next best is Langevin?
Thank you for your help & best regards,
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