[AMBER] TI calculations using pmemd

From: Roma Mukhopadhyay <roma1988.nmsu.edu>
Date: Wed, 4 Oct 2017 20:00:22 +0000

Hi ,

I am trying to repeat pKa calculation tutorial with Thermodynamic integration tutorial (Amber tutorial A6-section 1 and 2) using pmemd, but after explicit solvation of the molecule.

My step 1 output file gives me an error "Coordinate resetting (shake) was not accomplished within 3000 iterations ". The ntc and ntf are both set at 2.

I can't figure out where this error is coming from. Attached is the zipped folder containing the prmtop, inpcrd, the mdin and the output file.

I would really appreciate help regarding this matter.



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Received on Wed Oct 04 2017 - 13:30:02 PDT
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