RMSD metadynamics

From: simone bardwell (sbard79_at_gmail.com)
Date: Wed Feb 15 2012 - 13:25:16 CST


I have a couple of questions regarding setting up
metadynamics calculations in NAMD. I have looked though the archive user
list but have not found a response to my questions.

I would like to use RMSD as a CV for a metadynamics calculation. I would
like to be able to specify a start and end structure and then a set of
atoms to use to fit the structures together and then measure the rmsd of a
different region. I have read the Manual however am not sure if the region
being specified is for the fit and will also be the region to measure.

My second question is whether anyone has any practical examples of RMSD
metadynamics input files they would be willing to share. I have searched
for tutorial examples for these types of calculations however with no
success. To be able to refer to an example would be really helpful.

Kind regards,
Simone Bardwell

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