[AMBER] Question about thermodynamic integration.

From: <neildancer.sina.com>
Date: Mon, 23 Aug 2021 14:48:05 +0800

Dear, Amber community.
   I am tring to run the side chain-mini tutorial of thermodynamic integration using GPU 2080. Fortunately, the calculated result is similar with the tutorial. Then, I try to calculate the HIV protease and the drug APV with the same parameter setting. However, the dv/dl values are almost all postive. the deltaG sum for complex = 12.366411252470371, the deltaG sum for protein = 10.00340090677647. I have no idea whether this type result is normal or abnormal. In the tutorial calculation, the two deltaG value are both negative. Maybe the negative value is more reasonable. Please help me, thanks!


Ning Wang <PhD>
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences

My reseached interests has foucsed on protein structure determinated by Cryo-EM, virtual screening of potential drugs, protein molecular dynamic simulation, and protein design via computational biology.

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Received on Mon Aug 23 2021 - 00:00:02 PDT
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