On Mar 9, 2012, at 4:47 PM, David Minh <daveminh.gmail.com> wrote:
> As a test, I ran a short trajectory with sander and then used sander to reprocess the same trajectory to try to get the same energies. The prmtop and inpcrd files were the same. It was disturbing to see that the energies were different.
>
> In any case, is there a way to ensure that energies in the mdout file are consistent with the energies of the coordinates in the mdcrd file?
You've done it: use the imin=5 option, and you will get the energies that correspond to the
Coordinates in the mdcrd file. Try short runs with ntpr=1 to see more about what is going on.
You should also be able to use the ntwe option to dump energies, although I have never done that myself....
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 09 2012 - 18:00:03 PST
