From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sun Jul 05 2020 - 14:02:20 CDT
Equilibration with water is the same as with any other solvent in the
classical systems I've worked with. The only real practical difference is
that "wrapWater" no longer wraps your solvent for obvious reasons, so you
may need some PBC corrections to make for visualization purposes.
On Sun, Jul 5, 2020 at 8:27 AM Francesco Pietra <chiendarret_at_gmail.com>
> 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?
> On Sun, Jul 5, 2020 at 6:06 AM Josh Vermaas <joshua.vermaas_at_gmail.com>
>> Or if you don't care that it isn't a library, here is my methanol box.
>> On Sat, Jul 4, 2020 at 11:57 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
>>> 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?
>>> On Sat, Jul 4, 2020, 10:48 AM Francesco Pietra <chiendarret_at_gmail.com>
>>>> There 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 advice
>>>> francesco pietra
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