VMD-L Mailing List

From: Debasis Sengupta (dxs_at_cfdrc.com)
Date: Thu Apr 14 2011 - 12:07:56 CDT

Alex,
Thanks. I tried creating multiple representation of dynamics bond. For
example, to draw C and O bond, I set "type C O" and distance cut-off as
1.7A. However, it seems like it connects C-C and O-O which are below
1.7A, in addition to C-O that are below 1.7A. I just want to connect
C-O that are below 1.7A.
Thanks
Debasis
On 2/11/2011 2:00 PM, Axel Kohlmeyer wrote:
> you can define multiple dynamics bonds representations,
> each for groups of atoms.
>
> cheers,
> axel.
>
> On Fri, Feb 11, 2011 at 1:01 PM, Debasis Sengupta<dxs_at_cfdrc.com> wrote:
>> Hi,
>> I am looking for an option to set up different bond lengths for different
>> atom pairs. I am trying visualize a reactive MD trajectory and I used
>> "DynamicBonds" where there is an option (Distance Cutoff) to set a bond
>> length which seems to be a global setting. By setting it to a higher value,
>> say, 2.1A, connects anything that is up to 2.1A. How can I make, say, O-H as
>> 1.2A, Si-O as 2.1A, and Si-H as 1.6, so that only O-H up to 1.2A, Si-O up
>> to 2.1A and Si-H up to 2.6A are connected in all frame of the trajectory?
>> Setting a "Distance Cutoff" to 2.1A make O-H connected when they are larger
>> than 1.2A.
>> Thanks
>> Debasis
>>
>>
>
>