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Re: [lammps-users] USER-COLVARS package, i-PI: question about steered md and thermostats
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Re: [lammps-users] USER-COLVARS package, i-PI: question about steered md and thermostats

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 21 Dec 2017 14:34:15 -0500

On Thu, Dec 21, 2017 at 10:13 AM, Nicolas Künzel <nicolas.kuenzel@...7298...> wrote:

I am writing my masters thesis about quantum free energy differences using Jarzynski's equality. We are studying the double proton transfer in the Formic Acid Dimer (FAD). In order to do that I combined the i-pi server with DFTB+ for electronic structure calculations and with LAMMPS as a client including the Colvars module to perform steered md (SMD) in the stiff-spring limit. First of all we are just interested in the classical case to understand the basic mechanisms. Before I studied conformational changes in Alanine Dipeptide (ADP) to understand SMD. That worked actually quite well.

But now my problem: as I started studying the FAD I ran into problems and I am not really sure from which part they arise. When I change the friction coefficient of the Langevin thermostat I use, the barrier height obtained with SMD changes significantly. And I can't find a range of values for the coefficient where the free energy profile doesn't change. I actually hoped to find such a plateau.

Searching about the reasons for this behaviour I ran into this post in the namd mailing list:

There someone states that
"2 - Algorithms used to control temperature usually are not designed to handle systems in which external forces induce motions in a preferred direction.
The Langevin thermostat for instance, will apply a net (average) zero force to atoms that do not move on a preferred direction, but likely will introduce an artificial viscous drag to atoms that are being pulled. Thus, your force peaks will be larger.

3 - Some temperature control methods induced center of mass motion, which is not good when you have fixed reference points like in SMD."

Do you have experience with this? So are there problems using a Langevin thermostat due to the directional force?
And are there maybe ways to prevent that from happening?

​have you tried a different thermostat? LAMMPS has a whole zoo of them. while fix langevin is very convenient during equilibration (as it quickly achieves equipartitioning​ of energy, a prerequisite for equilibration), it does manipulate the dynamics. so for sensitive simulation methods, the time constant - after equilibration - should be so large, that the frictional damping has no significant impact. it would be simpler, though, to use a nose-hoover thermostat (after initial equilibration with fix langevin) and avoid direct manipulation of the velocity altogether.



Maybe you can make a great Christmas present since most parts of my thesis worked well until now but now I am stuck and it is not so much time left.

Thanks and kind regards,


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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.