Re: Use of Targeted MD vs. Colvars

From: Giacomo Fiorin (
Date: Wed Oct 19 2022 - 14:25:43 CDT

Hi Collin, if you know ahead of time that the TMD protocol as defined here
<> is sufficient
for your purpose, either implementation will work (NAMD's dedicated
function or a Colvars function). Colvars simply offers you a much broader
range of methods available, including more flexibility in defining the
alignment that minimizes the RMSD.

If you're trying to produce just an animation/movie of the transition, the
TMD method in should be sufficient.

Otherwise, you may want to step up and use a less crude biasing method
(umbrella sampling, metadynamics, ABF, ...) and/or use other collective
variables than the RMSD, which TMD assumes. Colvars offers quite a few.
Lastly, particularly for RNA, some of the developers of PLUMED have done a
lot of work with RNA, including developing other types of variables: this
has been brought up recently <;!!DZ3fjg!_q8HOMIHTp1pZSHtPEZHEjwk56PP3VnjkM69K9X8BT3b4IJFy7ThhNvgGFg7lhkCqCKdBjb2jIiNoNshr_Ymv0-Syw$ >
in the Colvars repository, and those papers are worth a read for sure.

Hope that helps,

This message discusses the usage of Colvars, a software library that is
distributed with NAMD, but is independently developed and maintained.
Please see;!!DZ3fjg!_q8HOMIHTp1pZSHtPEZHEjwk56PP3VnjkM69K9X8BT3b4IJFy7ThhNvgGFg7lhkCqCKdBjb2jIiNoNshr_aueoSpjg$   for further information.

This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST