ABF application

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Nov 08 2007 - 08:28:23 CST

Dear Jerome, Chris, NAMD users,

Is it possible in ABF to apply the biasing force on a different
direction than that of the reaction coordinate?

I was thinking to retrieve the force $force (along the reaction
coordinate (r.c.) in the "ABForce" procedure, then in ABFapply calculate
a new force $new_force as $force/cos(alpha) (alpha = the angle between
the direction of the r..c. and the direction of the applied force), and
then apply this force on the new direction (Fvec = [vecscale $new_force
$e_dir], where $e_dir = the unit vector of this direction).... In this
way the force acting on the r.c direction will still be $force which
will be used for the estimation of the free energy along the r.c. ...

Such an application would make sense if I want to define the reaction
coordinate as the projection of one vector v1 on a defined vector v in a
protein and then move the head of v1 towards the head of v, rather than
parallel to v ....

Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:43 CST