Hi All,
We are doing a thermodynamic integration (TI) calculation using pmemd for a system containing a box of ionic liquid and rare earth elements. We need to compute the free energy change associated with mutating one rare earth element (Nd) into another (Yb). We have prepared the parameter and restart files using ParmEd, and we are applying the softcore potential exclusively to the rare earth atoms.
But when we run the calculation for the same lambda values in two trials without changing anything, we get different trajectories. In one case both Nd and Yb atoms are superimposed and moving together, but in the other case, they are moving individually. Can someone explain why it is happening even though we do not change anything?
Thank you.
Kind Regards,
Sandaruwani Weerawarna
Graduate Student
Dr. Theresa Windus Lab
Department of Chemistry
Iowa State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 09 2024 - 12:00:02 PDT
