ABF with the RMSD colvar

From: George Patargias (gpat_at_bioacademy.gr)
Date: Fri Jun 07 2013 - 08:51:22 CDT


I would like to set up an ABF simulation to study the conformational change
of a protein using as a colvar the C-alpha RMSD of two conformational states.

What is the reason of defining the lowerwallconstant/upperwallconstant

I am not sure I understand the meaning of the hideJacobian option. Is it
to be switched on or off?

How can I decide on the value of the option fullSamples? By checking the
PMF convergence?

Is there anything else to check for this particular colvar?

Many thanks in advance.

Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27

Office: +302106597568

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:16 CST