[AMBER] Regarding an issue with Thermodynamic Integration calculation

From: Weerawarna Kurukulasooriy, Sandaruwani Tharaka \[CHEM\] via AMBER <amber.ambermd.org>
Date: Wed, 21 Aug 2024 17:53:03 +0000

Hi All,

I was trying to do a TI calculation to get the Free energy from Nd to Yb in an ionic liquid solution{ACT][BMI].When I visualize the last output corresponding to last lambda value it seems like the O atom of one acetate molecule is superimposed with the Yb atom. But the minimum bond distance between the central Yb atom and Acetate O atom should not be less than 2.0 angstroms. Can someone help me to find the reason for that and how to solve it? Really appreciate your help. Let me know if you need any more details or files.

Thank You

Kind Regards,

Sandaruwani Weerawarna
Graduate Student
Dr. Theresa Windus Lab
Department of Chemistry
Iowa State University


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Received on Wed Aug 21 2024 - 11:00:02 PDT
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