VMD-L Mailing List

From: William Ray (ray.29_at_osu.edu)
Date: Thu Sep 27 2012 - 10:51:44 CDT

Hmmm...

ufx, ufy and ufz seem to be correctly zeroed across the entire molecule when the force is removed.

Nonetheless, the molecule continues to fall apart, as though forces were still present.

Forgive me for not knowing the VMD internals well enough yet, but it looks like ufx/y/z are external forces? Is there another set of variables we could look at for full integrated per-atom forces?

Thanks much!
Will Ray

(Main< (ray) 32 % set sel [atomselect top "resid 2 to 10"]
atomselect18619

>Main< (ray) 33 % set force [$sel get {ufx ufy ufz}]
{0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {
0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}

>Main< (ray) 34 % set force [$sel get {ufx ufy ufz}]
{0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {
0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898} {-0.3580720126628876 -0.11941620707511902 0.15656539797782898}

>Main< (ray) 35 % set force [$sel get {ufx ufy ufz}]
{0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {
0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0} {0.0 0.0 0.0}

On Sep 27, 2012, at 11:15 AM, John Stone wrote:

> Hi,
> Can you use an atom selection and print out the active values of
> "ufx", "ufy", and "ufz" before and after you try and reset the
> forces to zero?
>
> I just read through the code, and the Mouse-based IMD code is indeed
> trying to zero-out the forces when you press the middle or right mouse
> buttons when applying forces to residues. It is possible that there's a
> bug in the code that manages the force list or that the residue case is
> following an unexpected code path, but we should be able to determine
> where the problem is by watching the values of ufx/ufy/ufz as it runs.
> You can use a callback to trigger the atom selection query/printing
> if you prefer.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Sep 27, 2012 at 10:57:52AM -0400, William Ray wrote:
>>
>> 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
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
>