Previous Thread
Next Thread
Print Thread
Selecting specific location from restart file
#38268 04/28/21 03:16 PM
Joined: Sep 2018
Posts: 10
C
ca4930 Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: Sep 2018
Posts: 10
I'd like to select individual frames from my equilibration run to start separate production runs. I've saved coordinates at various points of the equilibration and when using them to start the production runs I get an 'Energy Change Tolerance Exceeded ' error. I'm using an NPT ensemble and I'm thinking that the box size has changed which is resulting in the error. I was wondering if I could just read the equilibration restart file at a particular location in order to vary the starting point of the production run?

Re: Selecting specific location from restart file
ca4930 #38269 04/28/21 03:36 PM
Joined: Sep 2003
Posts: 8,580
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,580
Likes: 11
The restart file has complete information only for single time point, usually the last one in the corresponding trajectory file.

If you set up PBC via crystal first, you can read a single coordinate set directly from a trajectory file, and the unit cell size will be automatically updated. You would still have to assign new initial velocities in the usual way, however.

Another option is to save a velocity trajectory at the same frequency as coordinates, then read coordinates from the trajectory, read corresponding set of velocities into the COMP coordinate set, and use the DYNAmics option "IASVEL 0" to use those velocities to start a new simulation.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

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

PHP: 7.3.31-1~deb10u1 Page Time: 0.007s Queries: 18 (0.004s) Memory: 0.7183 MB (Peak: 0.7542 MB) Data Comp: Off Server Time: 2021-12-01 00:41:19 UTC
Valid HTML 5 and Valid CSS