From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Wed Apr 21 2021 - 06:01:05 CDT
Dear NAMD wizards,
The warning from the subject is a topic of many questions appearing on
this list, but I haven't found a single answer which would explain its
exact meaning and the conditions which trigger it. The usual answers are
that it signs some steric or topology problems and such reasons lead to
a quick crash due to divergence of movement integrations. But it does
not apply to my case.
In a case I am playing with - a sheet of graphene - NAMD produces
immense numbers of these warnings, which seem to be false. The dynamics
of the system is stable, no crash, setting cutoff and pairlist well
above the system size does not help. These messages are just annoying
filling 90% of the log size.
I want to use this graphene example as exercise for my students, and
this flood of warnings not only makes it look unprofessional, but what
troubles me more is that I am unable to explain it. Specifically:
* what exactly is "excluded globally" and what are the numbers reported?
* are there any other conditions apart from cutoff, pairlistdist and
steric problems, which I can change to silence this warning?
The first number reported in the warnings changes regularly but the
difference between them is rather huge, from 2340 vs 4593 when they
first appear during minimization to for example 3759 vs 4593 at the end
of dynamics.
From my current experience, the combination of graphene and CHARMM
forcefield is not optimal. I already learned that due to L-J
interactions between bound carbons (in-plane) I was getting huge excess
of VDW energy; this was mostly corrected with setting the 1-4 L-J
parameters to 0, but possibly all in-plane L-J interactions should be
discarded. Basically I use a copy of the parameters for standard CA type
(which is also duplicated for CGenFF multi-ring ligands) and it provides
all necessary parameters, I only changed the 1-4 part. Note that this
type uses regular dihedrals instead of impropers to stiffen the ring
plane, so I have generated the PSF with all planar dihedrals but without
impropers.
I will be grateful for any insight.
With regards,
Paweł Kędzierski
P.S. Summary of the system for which I reported the numbers above. Note
there are no hydrogens so "114 hydrogen groups" is confusing. Here I
fixed atoms on the edge of the sheet but without fixing the flood of
warnings is still there, only the numbers change.
Info: STRUCTURE SUMMARY:
Info: 603 ATOMS
Info: 867 BONDS
Info: 1659 ANGLES
Info: 3186 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 114 FIXED ATOMS
Info: 1467 DEGREES OF FREEDOM
Info: 603 HYDROGEN GROUPS
Info: 1 ATOMS IN LARGEST HYDROGEN GROUP
Info: 603 MIGRATION GROUPS
Info: 1 ATOMS IN LARGEST MIGRATION GROUP
Info: 114 HYDROGEN GROUPS WITH ALL ATOMS FIXED
Info: TOTAL MASS = 7242.63 amu
Info: TOTAL CHARGE = 0 e
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