Free energy calculation under external bias, (e)ABF/US/etc

From: Jim (
Date: Fri Apr 28 2017 - 20:25:57 CDT


I want to obtain free energy profiles of passages of molecules through
nanopore systems immersed in an external electric field. I can use
different free energy sampling schemes (cv-SMD/Jarzynski, (*)ABF, US,
US-REMD, etc) to obtain PMFs. I have a couple questions related to that and
to new NAMD releases:

1. Is there a method that is preferred (aiming at quantitative accuracy
while possibly ignoring computational costs)?

   - a) For example, in regard to ABF, what can (and should) be used in the
   current NAMD version 2.12 (or CVS 2.13): ABF vs eABF vs on-the-fly eABF vs
   gABF vs egABF vs ...?

I get confused between all these flavors and their applicability to the
particular problem/system of interest.

2. Release notes of NAMD 2.12 in regard to Collective Variable Module:


while a message from the mailing list from Mar 2015 reads:

This confuses me. If I want to go ahead with *new* ABF simulations under
external electric field (that will affect *all* atoms in the simulation box
regardless of CV), what should or should I not do to ensure accurate final

3. Again from the release notes:

   - "Scripting command "cvcflags" to optimize performance of complex

I don't understand where and how the command "cvsflags" is and can be used.
Is there an example usage?


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