Re: REST and Periodic Cell Issues

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 15 2019 - 08:53:14 CDT

Hi Robyn, that type of error usually occurs early on in the equilibration
of a system, when the unit cell fluctuations are larger. But especially
for a smaller system, occasional fluctuations and long-time changes may
break the patching design that NAMD assign at the start of the run. I've
seen it happen a few times, regardless of solute scaling.

Possible workarounds may be increasing margin (unless done so already) or
use shorter run segments (maybe packed into a long job for the queue
system) so that the patching subdivision is closer to the most current
shape of the unit cell.

Giacomo

On Thu, Aug 15, 2019 at 9:41 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> We ran REST2 on a small peptide that frequently crossed boundaries without
> any issues that I recall ( https://www.ncbi.nlm.nih.gov/pubmed/30888824 )--0000000000001ebd41059028343e--

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