[gmx-users] angle_restraints_z and -ddcheck

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jan 2 16:39:36 CET 2010


I have just started working with the [ angle_restraints_z ] portion of  
the code. My initial tests indicate that it works in my system.  
However, in some cases I am getting a fatal error that a pair  
interaction is too far apart to be calculated within domain  
decomposition. Although the error message refers to a bonded  
interaction,  in actuality this atomic pair is the two atoms that  
define my vector whose angle to the z-axis is restrained. I guess that  
the same code that requires "bonded interactions have been properly  
assigned to the domain decomposition cells" also requires this of the  
vector termini for angle_restraints_z.

I suspect that my solution is to use -noddcheck:

"For pair interactions and tabulated bonds that do not generate  
exclusions, this check can be turned off with the option -noddcheck."

although it seems zealous to turn off a useful global error detector  
in order to avoid a crash based on the spurious detection of a known  
group of only two atoms.

I'm interested first to see if anybody else has encountered this,  
second to ask if applying -noddcheck seems like a good idea, and third  
to suggest that angle_restraints_z not spawn this fatal error --  
unless it is indeed required (in which case I should not be turning  
off my ddcheck).

error message follows, wherein atoms 138 and 293 are those that define  
my angle_restraints_z, which looks like this:

[ angle_restraints_z ]
138 293 1 40 500 1

Thank you,


Error messages from the .log file:

Not all bonded interactions have been properly assigned to the domain  
decomposition cells

A list of missing interactions:
        Angle Rest. Z of      1 missing      1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
        Angle Rest. Z atoms  138  293           global   138   293

Program mdrun_openmpi, VERSION 4.0.5
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 110951 bonded interactions could not be calculated because  
some atoms involved moved further apart than the multi-body cut-off  
distance (1 nm) or the two-body cut-off distance (1 nm), see option  
-rdd, for pairs and tabulated bonds also see option -ddcheck

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