Re: REST and Periodic Cell Issues

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
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 ( https://www.ncbi.nlm.nih.gov/pubmed/30888824 ).

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

Best,
JC

On Aug 12, 2019, at 9:34 AM, Stix, Robyn (NIH/NHLBI) [F] <robyn.stix_at_nih.gov<mailto:robyn.stix_at_nih.gov>> 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?


Robyn

This archive was generated by hypermail 2.1.6 : Wed Sep 18 2019 - 23:21:10 CDT