Simulation in Collective sub-space

From: James Starlight (
Date: Tue Jun 25 2013 - 07:52:41 CDT

Dear Namd users!

I'm looking for possible way of the performing some sort of the steered
molecular dynamics in the essential subspace (which would be organized by
some lowest frequency modes obtained from the Principal components analysis
of the unbiased MD trajectory for instance). Some sort of that simulation
called as essential dynamics sampling has been implemented in Gromacs.
Now I'm looking for possible extension of such technique which would allow
me to perform methadynamics in collective coordinates with the Free energy
surfaces calculation along reaction coordinates (in that case collective
coordinates). I'll be thankful if someone provide me with some NAMD

Thanks for help,


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