Dear Miro,
I sincerely doubt that this issue has been fixed, even in AMBER 2024. Recently, I needed to restrain the positions of all heavy atoms in a protein, so I set ntr=1 and used REFC as the PDB-derived structure. Everything went fine during NVT heating, but as soon as I turned on the barostat, the coordinates in the saved restart file deviated much (~1A) from REFC, and the simulation crashed immediately at the beginning of the subsequent step.
I'm aware that always setting REFC as INPCRD is a workaround, but I still don't think this is a good solution, since deviations can accumulate from step to step.
Best regards,
Yunhao Mei
Am 16.11.2022 um 13:43 schrieb Miroslav Suruzhon via AMBER:
> Dear AMBER users,
>
> I have seen some past questions/issues about positional restraints not being compatible with constant-pressure simulations because the restraint positions are not scaled by the barostat. Is this still the case in AMBER 2022?
>
> Many thanks.
>
> Miro
>
> 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 Tue Feb 11 2025 - 20:00:02 PST
