VMD-L Mailing List

From: William Ray (ray.29_at_osu.edu)
Date: Thu Sep 27 2012 - 09:57:52 CDT

VMD 1.9.1 and NAMD 2.9 on MacOS 10.7.4

I'm seeing what seems to be a bug in IMD/AutoIMD when using the mouse to apply a force to a residue. Specifically, when the force is released in the interface, it doesn't actually appear to be removed from the simulation.

This is demonstrable with the deca-alanine tutorial PDB and PSF, using either the 10ala tutorial dedicated process, or loading the 10ala files and using AutoIMD.

When a force is applied to a single atom, 10ala stretches, h-bonds break, etc. Middle-clicking on the atom to which the force was applied makes the red force-arrow disappear, and 10ala generally "springs back". h-bonds reform, etc.

When a force is applied to a residue, multiple force-arrows appear, 10ala stretches, and even if I middle-click to remove the force immediately after the first h-bond breaks (all red force-arrows disappear), 10ala will continue stretching in the direction of the originally applied force, breaking all the other h-bonds until it is a stretched linear chain, and will never spring back. The interface does show zero for the applied force, after middle-clicking to remove it.

This happens nomatter how small a force I attempt to apply to a residue. If it's sufficient to break a single h-bond, even after middle-click removing the force, 10ala will be inexorably unfolded, never to regain structure.

My guess is that the middle-click is not deleting forces from all the atoms where a force was applied, but I don't know how to diagnose this further.

Yes, I'm working on getting a Phantom set up, but the mouse will have to do until I get a spare linux box for the office.

Any suggestions?
Will Ray
OSU Biophysics