statistical error in ABF calculations

From: Artur Hermano (
Date: Wed Mar 14 2018 - 10:27:15 CDT

Hello NAMD users,

I'm currently using ABF to measure the binding free energy of a protein-protein system. My simulations are divided into 2 angstroms windows and I am verifying convergence through progressively longer windows (5 ns, 10 ns, 15 ns and so on). I see convergence happening when I run 10 ns/window simulations because the RMSE (calculated from the .grad files of this run) compared to longer windows runs is considerably small.

My question is: how can I calculate the statistical error of an individual run? Without having to compare it with other runs.

I aim at having the error bars for each window of my run, but I have not yet figured out how to do this with NAMD 2.12.

Would someone please shed some light on how I can do this?

Thank you so much!

Artur Hermano
Mestrando em Biologia Computacional e Sistemas
Instituto Oswaldo Cruz

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:19:45 CST