On Mon, Sep 09, 2024, Weerawarna Kurukulasooriy, Sandaruwani Tharaka [CHEM] via AMBER wrote:
>
> 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?
This is indeed odd. One thing that might help is to examine the two mdout
files side by side using a file comparison tool like vimdiff. There might
be some differences that point to what is happened.
If you just want to change Nd to Yb, no softcore should be needed. In that
case, there is only one rare earth atom, which is changing its character
from Nd to Yb as lambda changes. See if that might help.
....dac
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Received on Thu Sep 12 2024 - 07:00:03 PDT
