Dear Miro,
I am one of the persons who previously asked about this in the mailing
list, since I did NpT simulations with restraints in previous Amber
versions - to prepare the system for the GIST method.
In previous versions, the NpT simulations run fine if only one molecule
has positional restraints. If two molecules (e.g., two protein chains)
have restraints, the barostat tries to move them relative to each other.
Since this produces a high energy, the volume cannot equilibrate
properly. This can be avoided by modifying the topology file such that
all restraint molecules are treated as one "molecule". There don't need
to be any bonds between them, just modify the SOLVENT_POINTERS and
ATOMS_PER_MOLECULE.
I am not completely up-to-date on the changes in Amber22, but I would
assume that the situation is still the same. If not, I hope that someone
can correct me.
This is my old question in the mailing list:
http://archive.ambermd.org/201906/0295.html
Best regards,
Franz Waibl
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 Thu Nov 17 2022 - 05:30:02 PST
