From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Tue May 05 2020 - 14:49:42 CDT
Any input is much appreciated on how to overcome instability and start production run.
From: Khoualdi Asma Feriel
Sent: May 3, 2020 4:05 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: Rattle algorithm error: when to minimise
Dear NAMD users,
I have encountered ERROR: Constraint failure in RATTLE algorithm for atom ..! at the production run.
I have searched the mailing list for ERROR: Constraint failure in RATTLE algorithm for atom ...!
and found that some of the solutions suggest that I need to minimize the system more. I have finished six equilibration steps already and done minimisation only in first step6.1 for 1000 steps. My question is: is it okay to minimise the system now at the last equilibration step 6.6 ?
The equilibration steps take so long (about 8-10 days) to finish all six so I don't want to start again from step 6.1 to change minimisation for that step.
Attached is my RMSD for the equilibration trajectory.
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