VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Mon Jul 16 2012 - 13:16:32 CDT

Thanks for quick response.
The short answer is yes I'd like you to add an extra tab that allows me
to use on of my graphics selections.
Then I can select whatever I want

Long answer

I have a sensable phantom omni device so I guess I can do this on mky
desktop
But what I really want to do is IMD demo's w/ a Little Fe portable
parallel computer (http://littlefe.net)

For this I use my laptop (no 6DOF device... just mouse) as the graphics
front end and the Little Fe
as the compute nodes.

choices seem to be
1) get sensable to work w/ my laptop (that would make a better demo) but
I'd have to lug around a lot of stuff but it's all in name of science so....

2) If I'm limited to atoms,residues, fragments I can redefine my
molecular structures to have the necessary hooks,
(ligand receptor systems work great for this already)
but I'd prefer to have arbitrary selections.

3) another alternative would be to do some sort of steered MD rather
than IMD... but demo is not as fun.

Thanks
TOm

On 07/16/2012 11:44 AM, John Stone wrote:
> Hi,
> As far as the mouse goes, what Axel says is correct. However, if
> you are using a 6DOF input device via the Graphics|Tools menu, you can
> apply forces to an arbitrary atom selection by using the "assigned rep"
> tab, and selecting the appropriate molecule and representation to apply
> the forces to. This gives you the ability to use any selection you want,
> though it will have to be associated with a graphical representation.
>
> Let me know if this is what you're after, or if you really want something
> that also works for the mouse based interface.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jul 16, 2012 at 06:25:49PM +0200, Axel Kohlmeyer wrote:
>> On Mon, Jul 16, 2012 at 5:25 PM, Thomas C. Bishop<bishop_at_latech.edu> wrote:
>>> When doing IMD w/ VMD one can use the GUI to select
>>> atom, residue or fragment for applying forces during IMD
>>>
>>> Can the atomselections commands be used in a text console
>>> to pick groups of atoms to which the force will be applied?
>> no.
>>
>> atom/residue/fragment are how the force of the effector
>> is applied and is more like a "pick" option than a selection.
>>
>> axel.
>>
>>
>>> The atom,residue,fragment options are too limited for my task.
>>>
>>> Thanks in advance for any info
>>>
>>> TOm
>>>
>>> --
>>> *******************************
>>> Thomas C. Bishop
>>> Tel: 318-257-5209
>>> Fax: 318-257-3823
>>> www.latech.edu/~bishop
>>> ********************************
>>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
*******************************
    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823
    www.latech.edu/~bishop
********************************