From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Thu Apr 22 2021 - 08:21:08 CDT
Thank you for detailed explanation.
Increasing the margin to e.g. 3.0, which is more than ring diameter,
After several more tests I think, I am triggering a bug in this global
exclusion checksum calculation.
My grafene was generated idealized with all Z coordinates exactly 0.0,
and that was the source of the problem.
When I started calculations using coordinates from final MD frame of
previous job, so they were slightly distorted, NOT EVEN A SINGLE WARNING
appeared. On the other hand, when I start from ideally flat sheet
aligned to XY plane, I am getting this warning at virtually every step.
The checksum have not to be calculated from scratch, only updated, and
some initial mistake is never corrected later; apparently such update
occurs once per cycle (20 steps in my case).
The warnings are issued both during minimization and dynamics but namd
continues anyway, I run tests for 100ps with no problem.
I also checked whether the problem is triggered due to zero Z thickness
of the entire system; but adding a sodium ion like 5A above the graphene
did not help.
So my workaround now is to generate the graphene coordinates with
minimal random distortion (-0.05 to +0.05A range) out of the XY plane
and voila, no more warnings :-D.
W dniu 21.04.2021 o 22:31, David Hardy pisze:
> Hi Pawel,
> NAMD calculates certain checksums to make sure that, due to its
> parallel decomposition, no terms are accidentally dropped during force
> evaluation. The “global exclusion” checksum counts the total number of
> non-bonded exclusions evaluated, where the exclusion policy is set in
> the config file (usually “exclude scaled1-4” for CHARMM FF). Before
> the simulation begins, NAMD counts the total number of non-bonded
> exclusions that it should be evaluating when computing the force. It
> will then report when an undercount occurs. The numbers reported are
> the checksum vs. the number of exclusions that should have been
> evaluated. Since this does not end your simulation, this must be
> occurring for you during minimization. If this were to occur during
> dynamics, NAMD would terminate with an error.
> So why would this be occurring? Well, in order for an exclusion to be
> calculated, the pair of atoms being excluded must be in an adjacent
> pair of patches. It sounds like your graphene sheet has carbons spaced
> far enough away, that you have exclusions due to a covalently bonded
> chain of 3 or perhaps 4 carbon atoms that extend beyond an entire
> patch. To avoid these messages, one thing you might try doing is
> artificially increasing the patch size by setting “margin” to a
> nonzero value large enough to pad the patches so that these 3-chains
> or 4-chains of carbon atoms are kept in adjacent patches.
> As to the “hydrogen group” designation, NAMD, for performance reasons,
> keeps each hydrogen atom together with its heavy parent atoms, and
> refers to the resulting clusters as “hydrogen groups.” In your case,
> every carbon atom would be its own hydrogen group (and migration
> group). Since this has important meaning for biomolecules, we report
> aspects of these clusters, such as the “114 hydrogen groups with all
> atoms fixed” message.
> Best regards,
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>,
>> On Apr 21, 2021, at 6:01 AM, Pawel Kedzierski
>> <pawel.kedzierski_at_pwr.edu.pl <mailto:pawel.kedzierski_at_pwr.edu.pl>> wrote:
>> 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
>> * 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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