[AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ?

From: Chris Neale <candrewn.gmail.com>
Date: Fri, 26 Jan 2018 12:48:09 -0700


I'd like to restrain part of a protein that is simulated in a box of water
and avoid any artifacts from pressure coupling. Therefore, I'd like to
never scale or shift the coordinates provided to pmemd via -ref and have
the restraints at all simulation steps be independent of whether or not
there have been restarts between those steps.

To implement the restraints, my pmemd -i file contains:

I saw some suggestion by Tom C. that this might be possible via code
modification here: http://ambermd.org/Questions/mail/303.html
"(2) Alter runmd.f to NOT call ew_pscale IF ntr.gt.0 (i.e. comment out two
lines of code)."
but that advice is 10+ years old and amber16 seems not to have a file
called runmd.f.

I also see that belly could be used in place of restraints, but that does
not work on GPUs in amber16.

I also see that there perhaps used to be a variable npscal=1 that would
scale only the center of mass of each molecule during pressure coupling,
but I can't find any reference to that parameter in the amber16 manual.

So, is amber16 capable of rigorously combining pressure coupling with
position restraints on more than one atom, especially given potential
simulation restarts? I realize that there are some workflows in which the
problems might not be horrendous, but I'm really hoping there is a
completely proper way to do this.

The ability to never scale reference coordinates is probably what I'm after.

Thank you very much for your suggestions,
AMBER mailing list
Received on Fri Jan 26 2018 - 12:00:03 PST
Custom Search