Re: Alchemify?

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Feb 19 2018 - 09:32:33 CST

Hi Randy,

On 19 February 2018 at 16:03, Randy J. Zauhar <r.zauhar_at_usciences.edu>
wrote:

> Hi Jerome,
>
> Sorry, I am picking you individually, as I see your name associated with
> the issue I want to ask about. ;-)
>

Even if the question is for me, it's better for the community to have this
conversation in the searchable mailing list archives. So I hope you don't
mind if I add the list in CC.

In my recent posts I proposed making my simulation more reversible by
> having solvent in the active site disappear while ligand appears, but I
> realize now that nonbonded interactions between in-coming and out-going
> groups are not automatically excluded in NAMD.
>

What makes you think that? In principle they should be... Are you using a
memory-optimized build? (typically reserved for huge systems, so not likely
for alchemical simulations)

> I see a number of references to a tool called alchemify that would seem do
> exactly what I need, but it does not seem to be available anymore, and is
> called ‘deprecated’.
>

Although alchemify should rarely be necessary now, I've moved it here to
keep it available:
https://github.com/jhenin/alchemify

> Supposedly you can do all this in NAMD now - but how? Or do I need to
> somehow modify the PSF?
>

Alchemify will modify the PSF for you.

Best,
Jerome

> Any advice much appreciated!
>
> Randy
>
> Randy J. Zauhar, PhD
>
> Prof. of Biochemistry
>
> Dept. of Chemistry & Biochemistry
> University of the Sciences in Philadelphia
> 600 S. 43rd Street
> Philadelphia, PA 19104
>
> Phone: (215)596-8691
> FAX: (215)596-8543
> E-mail: r.zauhar_at_usciences.edu<mailto:r.zauhar_at_usciences.edu>
>
>
>
> “Yeah the night is gonna fall, and the vultures will surround you /
> And when you’re lookin’ in the mirror what you see is gon’ astound you"
>
> — Death Cab for Cutie, “Monday Morning"
>
>
>
>

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