Re: REST and Periodic Cell Issues

From: Gumbart, JC (
Date: Thu Aug 15 2019 - 08:39:56 CDT

We ran REST2 on a small peptide that frequently crossed boundaries without any issues that I recall ( ).

This doesn’t sound like something specific to REST2. Can you replicate the error in a single run with or without solute scaling?


On Aug 12, 2019, at 9:34 AM, Stix, Robyn (NIH/NHLBI) [F] <<>> wrote:

Has anyone experienced any issues when running REST2 with periodic boundary conditions and the solute being scaled is close to or passes through the periodic boundary? Such as getting a FATAL ERROR: periodic cell has become too small for original patch grid (200ns into a production run). If so, is there a way to fix this besides adding center-of-mass constraints to the solute to keep it away from the edge of the box?


This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:54 CST