From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Mar 16 2021 - 13:31:53 CDT
Dear Geo,
Introducing an external force between the centers of mass of various subsets of atoms is possible through the Colvars module. There is good documentation available https://www.ks.uiuc.edu/Research/namd/2.14/ug/node53.html <https://www.ks.uiuc.edu/Research/namd/2.14/ug/node53.html>.
Since this force is being applied to centers of mass, there is no mechanism for calculating what you want by simply changing the force field parameter files.
Best regards,
Dave
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Mar 12, 2021, at 2:54 PM, Ropon-Palacios G. <biodano.geo_at_gmail.com> wrote: > > Dear namd user, > > How can add LJ 12 6 E (r) = 4ε[(σ/r) − (σ/r) ] this respulsive potential where ε = 10−3 kJ/mol, σ = 20 Å, and r is the distance between the centers of mass of the ligands? > > How add this in rtf or parm files? > > Best, > > Geo.
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST