From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Feb 27 2013 - 15:29:49 CST
Thanks for doing the research. Because you're in a vacuum, the temperature is much harder to control. In water, I've gotten reasonable results with 0.1. For example, with T = 323 K (target), I get 324.5 +/- 1.9 K over many nanoseconds.
On Feb 27, 2013, at 12:29 PM, Ajasja Ljubetič wrote:
> Tried with 0.1, but I think its a bit too little. But I get the general gist, that the LD thermostat can be tuned to produce minimal distortion to diffusion.
> Best regards,
> 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
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