On Sat, Sep 12, 2020, pietroa.bii.a-star.edu.sg wrote:
>Here is a small example. It is a prmtop based alchemical scheme where
>the system is simulated with progressively different prmtops to alter
>the geometry of the system. In this case, the intended outcome is to
>"grow" a glycine right after the alanine. The system fails with pmemd,
>but it works perfectly fine with sander. The attached prmtop and
>inpcrd represent the first step of the simulation.
Can you send an mdin file as well as the exact flags you gave to the
programs? If I run a short simulation with with your files, with
either sander or pmemd, I see no errors.
...thx...dac
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Received on Thu Sep 17 2020 - 06:30:02 PDT
