Re: reconstructing pmf

From: Vermaas, Joshua (
Date: Mon Dec 18 2017 - 18:35:31 CST

Hi Stefano,

I haven't done it myself, but wouldn't you just need to write a script to re-add the hills that metadynamics is adding yourself, based either on the colvars.traj file (ideally) or worst case recalculating your reaction coordinate trajectory from the dcd? The end result should in principle be the same if you saved these values at the same frequency that hills are added, albeit with a large chance of making a mistake somewhere in code if you don't have a working example to make sure that your script does what it is supposed to.


On 12/18/2017 05:29 PM, Stefano Guglielmo wrote:
Dear NAMD users,
is it possible to reconstruct pmf of a metadynamics simulation (if for some reason the original file was corrupted or lost) in the same format as the one written as output by NAMD?
Thanks in advance

Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:45 CST