VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Wed Nov 12 2014 - 17:54:44 CST

Hi,

1- For atoms selection:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html

2- For H-bonds, see:

http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
or
http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/

3- For MSD, I found this:

http://multiscalelab.org/utilities/DiffusionCoefficientTool

Regards
M

On Thu, Nov 13, 2014 at 6:52 AM, Bharat Sharma <bharatsolbridge_at_gmail.com>
wrote:

> Hello again,
> I figured it out how to call functions to select atoms, but how to deal
> with Periodic atoms and calculate hydrogen bonds within selection only?
>
> Thank you.
>
> Bharat
>
> On Wed, Nov 12, 2014 at 1:38 PM, Bharat Sharma <bharatsolbridge_at_gmail.com>
> wrote:
>
>> Hello Experts,
>>
>> I am interested in doing some MSD analysis for subset of my simulation
>> box. Basically I want to call different functions on TCL window. I have
>> some questions regarding calling VMD subroutines on TCL window.
>>
>> How do I call the functions to do following tasks?
>> 1) to call selected atoms (for example: name O within 3 of index 123)
>> 2) number of hydrogen bonds within selection
>> 3) MSD of selected systems.
>>
>> Any suggestions are expected very helpful and appreciated.
>>
>> Thank you.
>>
>> Bharat
>>
>
>