Dear AMBER users,
I have been having issues when running vacuum free energy simulations in pmemd (AMBER 2022). This only occurs when I add the flag igb=6 to my MDIN file, but as far as I understand, this is needed to obtain correct results. However, if I use igb=6 together with ifmbar=1, I get segmentation fault but I don’t when I set ifmbar=0.
I would like to get the correct MBAR output in the vacuum leg to keep the run consistent with the solvated leg, so it is highly preferable to keep ifmbar=1. Does anyone know what the correct set of MDIN parameters would be for running an MBAR calculation in vacuum? I am attaching a zip file containing a simple benzene~toluene perturbation and an MDIN file that segfaults unless one turns off ifmbar.
Any input would be highly appreciated.
Kind regards,
Miroslav

Miroslav Suruzhon MSc PhD
Molecular Dynamics Research Scientist
+44 (0) 7719 025700
Exscientia
The Schrödinger Building, Heatley Road, Oxford Science Park, Oxford, OX4 4GE
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Received on Wed Jan 25 2023 - 09:30:02 PST
