**From:** Ajasja Ljubetič (*ajasja.ljubetic_at_gmail.com*)

**Date:** Thu Apr 03 2014 - 07:36:28 CDT

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Dear all,

When doing *free energy* calculations the *original dynamics of the colvars

is lost* as it is perturbed by the added bias. So it seems one can get

either free energy (by applying a bias) or dynamics (rate constants for

transition between states) using unbiased MD.

Wouldn't it be nice if it were possible to *obtain rate constants from free

energy calculations* as well? It turns out that this is indeed possible

under the assumptions that the colvars undergo Brownian

motion<http://en.wikipedia.org/wiki/Brownian_motion>(i.e. the colvars

behave diffusively). The reason behind this is that the

bias does not perturb the diffusive motion of the colvars.

A few *hundred nanosecond-long biased MD* trajectory can be* extended to

millisecond* lengths in the colvars subspace at a very small additional

computational cost. First one runs the biased MD simulation to obtain the

free energy. From the biased MD trajectory of the colvars, *position

dependent diffusion coefficients *are extracted. The free energy and the

diffusion coefficients are used to simulate very long colvar trajectories.

*>From the long colvar trajectories rate constants and other dynamics data
*

can be obtained.

(Side note: existing biased MD trajectories can be analyzed as well).

The tricky part is obtaining position-dependent diffusion coefficients.

This is the problem we tackled

recently<http://scitation.aip.org/content/aip/journal/jcp/140/8/10.1063/1.4866448>

(J. Chem. Phys. 140, 084109 (2014); a PDF is available on our

website<about:invalid#zClosurez>).

We also provide an open source

Package<http://scitation.aip.org/content/aip/journal/jcp/140/8/10.1063/1.4866448>

for

calculating position dependent diffusion coefficients and generating long

diffusive trajectories.

Since many people are using NAMD with ABF or metadynamics calculations to

estimate free energies, I hope this e-mail (and the package) are useful.

Best regards,

Ajasja Ljubetič

Young researcher

Laboratory for biophysics <http://lbf.ijs.si>

Institute Jozef Stefan, Slovenia

*Disclaimer*: In case it is not clear -- I'm the author of the mentioned

paper and package.

High level questions (eg. is this diffusive approximation even useful?:)

are probably on topic for the mailing list, but *low-level stuff* (eg.

problems with installations, etc...) should be addressed directly to me *off

the mailinglist*.

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