Previous Thread
Next Thread
Print Thread
time series of distance between two atom selections
#36985 06/05/18 08:26 AM
Joined: May 2007
Posts: 46
N
Nadia Offline OP
Forum Member
OP Offline
Forum Member
N
Joined: May 2007
Posts: 46
Dear all,
I would like to calculate a time series of the distance between the center of mass of two atom selections. For example, using correl something like

correl ...
enter group1 atom sele atoms1 end mass
enter group2 atom sele atoms2 end mass
traj ...

Is something like this possible or do I need to use a different approach?

Re: time series of distance between two atom selections
Nadia #36986 06/05/18 03:05 PM
Joined: Sep 2003
Posts: 8,501
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,501
Yes, but you then need to use MANTIME commands to get the difference vector, and to compute the vector length time series.

It may be easiest to break the coordinate tuple into the components, e.g. for group1:

enter g1x atom x sele atoms1 end mass
enter g1y atom y sele atoms1 end mass
enter g1z atom z sele atoms1 end mass

That way, it's straightforward to compute r from sqrt(x**2 + y**2 + z**2) with MANTIME commands.


Rick Venable
computational chemist

Re: time series of distance between two atom selections
Nadia #36987 06/06/18 07:37 PM
Joined: May 2007
Posts: 46
N
Nadia Offline OP
Forum Member
OP Offline
Forum Member
N
Joined: May 2007
Posts: 46
Many thanks!


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.005s Queries: 20 (0.002s) Memory: 0.9024 MB (Peak: 0.9777 MB) Data Comp: Off Server Time: 2020-10-21 08:21:25 UTC
Valid HTML 5 and Valid CSS