From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Dec 18 2003 - 13:03:01 CST
Hello Jan,
Sorry for the late reply to you and the list.
As it turns out I had several problems. The one causing this error was my
box size not being big enough. The others were MPI buffer errors and a
required optimization in the load balancer.
Brian
On Thu, 27 Nov 2003, Jan Saam wrote:
> Brian,
>
> this happened to me, too. It has been a while ago, but I think the
> reason was an incorrect topology definition of a residue patch that I
> generated myself. I defined a bond twice, once in the original residue
> and once in the patch.
> Another typical reaction of namd to that is the detection of margin
> violations.
>
> Below is a little script that checks a structure for double defined
> bonds.
>
> Good luck,
> Jan
>
>
> --------------------------
> Jan Saam
> Humboldt-University Berlin
> Charité (medical school)
> Institute for Biochemisty
> Monbijoustr. 2
> 10117 Berlin
> Germany
> phone: +49 30 450 528 449
>
>
>
> proc checkbonds { sel } {
> set indexlist ""
> set i 0
> set bonds [$sel getbonds]
> set index [$sel list]
> set molid [$sel molid]
> foreach b $bonds {
> set compressed [lsort -real -unique $b]
> if {[llength $b]!=[llength $compressed]} {
> set atom [atomselect $molid "index [lindex index $i]"]
> set res [$atom get resname]
> set resid [$atom get resid]
> set name [$atom get name]
> set seg [$atom get segname]
> puts "seg $seg: $res$resid $name : $i: $b"
> lappend indexlist $i
> }
> if {! $i%1000} {puts $i}
> incr i
> }
> return $indexlist
> }
>
>
> Am Do, 2003-11-27 um 00.57 schrieb Brian Bennion:
> > Hello,
> >
> > Has anyone seen this error before? My system is quite large but I know
> > others have done larger.
> > Below is a snippet of the log file.
> >
> > Brian
> >
> >
> > nfo: ****************************
> > Info: STRUCTURE SUMMARY:
> > Info: 4877547 ATOMS
> > Info: 3251698 BONDS
> > Info: 1625849 ANGLES
> > Info: 0 DIHEDRALS
> > Info: 0 IMPROPERS
> > Info: 0 EXCLUSIONS
> > Info: 14632638 DEGREES OF FREEDOM
> > Info: 1625849 HYDROGEN GROUPS
> > Info: TOTAL MASS = 2.92903e+07 amu
> > Info: TOTAL CHARGE = 0 e
> > Info: *****************************
> > Info: Entering startup phase 0 with 749551 kB of memory in use.
> > Info: Entering startup phase 1 with 749551 kB of memory in use.
> > Info: Entering startup phase 2 with 1054811 kB of memory in use.
> > Info: Entering startup phase 3 with 1092919 kB of memory in use.
> > Info: PATCH GRID IS 11 (PERIODIC) BY 11 (PERIODIC) BY 11 (PERIODIC)
> > Info: REMOVING COM VELOCITY 0.000438623 -0.000183485 0.000199183
> > BUG ALERT: Mother atom with hydrogenGroupSize of 0!
> > BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
> > BUG ALERT: Mother atom with hydrogenGroupSize of 0!
> > BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
> > [0] MPI Abort by user Aborting program !
> >
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** *****************************************************************
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