Re: namd 2.7b: measure free energy difference "growing" a force constant

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Sat Jun 20 2009 - 14:01:30 CDT

Sebastion,

The old Free Energy module is currently the only way to directly perform a
TI-of-force-constants.

With the contribution of the Colvars code, we (the NAMD developers) debated
depreciating the Free Energy module but realized this would be disruptive to
those already using that module. We therefore removed it's documentation
from the userguide but left the actual code in place. So the Free Energy
module is actually still available, just use commands as defined in the 2.6
manual.

The Free Energy module will be present in the official release of NAMD 2.7.
We will make a final decision about the depreciation of the Free Energy
module at some point in the future. If we do decide to depreciate this
module, other modules will provide full redundancy so there will not be a
loss of functionality in NAMD which you might be using in your simulations.

Please let us know if there are specific functionalities in the Free Energy
module you would like to insure are not lost should we ultimately decide to
fully depreciate this module.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Sat, Jun 20, 2009 at 9:33 AM, Sebastian Stolzenberg <
s.stolzenberg_at_gmail.com> wrote:
> Dear All,
>
> sorry I might have missed this piece of info:
> In namd 2.6, with the old PMF module (manual, p. 87), I could measure free
> energy differences, "growing" a force constant on a particular restraint.
>
> In namd 2.7b, what module can I use instead to have full support again? ABF
> in the colvar? ... how :) ?
>
> Thank you,
> Sebastian
>
>

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