|From:||Axel Kohlmeyer <akohlmey@...24...>|
|Date:||Thu, 21 Dec 2017 14:34:15 -0500|
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: http://www.ks.uiuc.edu/
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?
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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