From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Oct 19 2022 - 14:25:43 CDT
Hi Collin, if you know ahead of time that the TMD protocol as defined here
<http://www.ks.uiuc.edu/Research/namd/2.14/ug/node47.html> 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 <https://urldefense.com/v3/__https://github.com/Colvars/colvars/issues/495__;!!DZ3fjg!_q8HOMIHTp1pZSHtPEZHEjwk56PP3VnjkM69K9X8BT3b4IJFy7ThhNvgGFg7lhkCqCKdBjb2jIiNoNshr_Ymv0-Syw$ >
in the Colvars repository, and those papers are worth a read for sure.
Hope that helps,
Giacomo
-- ------------------------------------------------------------------------ This message discusses the usage of Colvars, a software library that is distributed with NAMD, but is independently developed and maintained. Please see https://urldefense.com/v3/__https://colvars.github.io__;!!DZ3fjg!_q8HOMIHTp1pZSHtPEZHEjwk56PP3VnjkM69K9X8BT3b4IJFy7ThhNvgGFg7lhkCqCKdBjb2jIiNoNshr_aueoSpjg$ for further information. ------------------------------------------------------------------------
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