Re: Equilibrated boxes of organic solvents

From: Joseph Farran (
Date: Sun Jul 05 2020 - 10:34:44 CDT

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-------- Original message --------From: Francesco Pietra <> Date: 7/5/20 7:37 AM (GMT-08:00) To: Josh Vermaas <> Cc: NAMD list <> Subject: Re: namd-l: Equilibrated boxes of organic solvents Thanks a lot for the gift.I am the first time at nonaqueous solvents, for QM-MM with small organic molecules cgenff for charmm36. Is any special flag with methanol for MD equilibration and QM-MM?francescoOn Sun, Jul 5, 2020 at 6:06 AM Josh Vermaas <> wrote:Or if you don't care that it isn't a library, here is my methanol box.-JoshOn Sat, Jul 4, 2020 at 11:57 PM Josh Vermaas <> wrote:Not that I'm aware of. I've got scripts to build initial boxes that need to be equilibrated. Usually doesn't take more than a nanosecond to get to a consistent density. Would that work for you?JoshOn Sat, Jul 4, 2020, 10:48 AM Francesco Pietra <> wrote:HelloThere are exhaustive indications on this forum how to prepare equilibrated boxes of organic solvents for NAMD with CHARMMFF. However, to avoid duplication of efforts, I am looking for a library of already equilibrated boxes, in particular of methanol. To be used with CGenFF not for biopolymers.Thanks for advicefrancesco pietra

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