[AMBER] reference potential alchemical calculation

From: Pietro Vidossich via AMBER <amber.ambermd.org>
Date: Wed, 1 Nov 2023 01:34:42 +0000

Dear Amber developers and users, hope all is fine with you.

Iím writing to ask advice on the setup of a reference potential alchemical calculation transforming a pyridine from MM to QM potential in a box of MM water molecules. The way I understand it, is to have an empty qmmask (and ifqnt=1) for the MM calculation (in the manual I read that the qmmask selection can be empty). Doing so I receive the error:

QM ATOM VALIDATION: nquant has a value of 0

SANDER BOMB in subroutine validate_qm_atoms

nquant illegal

Need 0 < nquant <= natom

Instead if I set ifqnt=0 for the MM simulation, the calculation remains stuck at the very beginning (is active but does not produce any MD step).

I checked that the calculation runs and completes with icfe=1 and ifqnt=1 using the same or different (but not empty) qmmask selections in the two simulations.

I would kindly ask about the correct way to setup such calculation, which I read in the literature is available in sander.

Thank you in advance.

Best regards,

Pietro Vidossich

MMDD group

IIT, Genova, Italy
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Received on Tue Oct 31 2023 - 19:00:02 PDT
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