VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jan 05 2015 - 00:54:35 CST

Look for keywords "constraints" "consref" "contraintscaling". RigidBonds is
only used to keep the hydrogens in place which allows using a timestep as
large as 1-2 fs.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Sindrila Dutta Banik
> Gesendet: Montag, 29. Dezember 2014 17:19
> An: vmd-l_at_ks.uiuc.edu
> Betreff: vmd-l: How to constrain a atom
>
> Dear All,
>
> I want to simulate a protein placed in a water box. For the same I
> first I
> want to minimize the total system with constrained on alpha carbon
> atom.
> But how could I mention the constrain in the input file.
>
> As I understood form the manual the 'rigidBonds' command is used to
> apply
> constrain a bond. But how to constrain a atom; please help me out.
>
> With best regards
> Sindrila Dutta Banik
>
>
> --
> Sindrila Dutta Banik
> C/O Prof. A. Chandra
> Project Scientist
> Department of Chemistry
> IIT Kanpur
> UP 208016