From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Feb 27 2013 - 11:29:28 CST
Tried with 0.1, but I think its a bit too little <http://pbrd.co/YXVC0F>.
But I get the general gist, that the LD thermostat can be tuned to produce
minimal distortion to diffusion.
On 25 February 2013 23:32, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Just to be sure, you weren't using multiple time-stepping, right? Because
> MTS doesn't conserve energy either.
> Langevin with a very low damping constant should be okay (try 0.1 to see
> if it works).
> On Feb 25, 2013, at 8:07 AM, Ajasja Ljubetič wrote:
> Dear all,
> 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,
> Lowe-Andersen, ...)
> 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,
> Ajasja Ljubetic
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:59 CST