update: segmentation faults with AMBER topology and RAMD tcl scripts

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Tue Feb 23 2010 - 08:31:27 CST

Dear all,

To test the errors I've been commenting on recently I compiled today's
CVS code of NAMD (23 February 2010) using exactly the same protocol as
for my last running compilation (13 August 2009). Tcl version is
tcl8.4.19. Architecture: x86_64 + infniband + intel 11.0 compiler +
mvapich1.4rc1. The compilation worked absolutely fine.

Then I ran the RAMD tests which resulted in "Segmentation violation" .
Then I tested the new executable for one of my standard MD simulation
using AMBER topology. The same undefined error occurred.

To conclude, the latest CVS code produces segmentation faults on AMBER
topologies regardless whether RAMD is switched on or not. Therefore,
this error apparently has nothing to do with the RAMD scripts. It looks
as if the amber topology is read correctly but the program exists with
segmentation violation immediately after reading the topology (below
last lines of the output)

I could not test against CHARMM topologies as I don't have one but
another NAMD user mentioned recently that the code runs fine on CHARMM
topologies while observing the same errors with AMBER topologies.

To test the RAMD scripts until the problem with the AMBER topologies
will be fixed, I suggest to compile namd 2.6 against tcl8.4.19 or above.
If you still see errors, please let me know.

Cheers
Vlad

-----------------output sample------------------------------
Reading parm file (1r9o_1.top) ...
PARM file in AMBER 7 format
Warning: Encounter 10-12 H-bond term
Warning: Found 18886 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 62 BONDS
Info: 131 ANGLES
Info: 49 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 210 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 0.158216
Info:
Info: Reading from binary file 1r9o_1_eq10_rst.500000.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 64265 ATOMS
Info: 64360 BONDS
Info: 13994 ANGLES
Info: 29662 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 98534 EXCLUSIONS
Info: 60475 RIGID BONDS
Info: 132320 DEGREES OF FREEDOM
Info: 22676 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 22676 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 394234 amu
Info: TOTAL CHARGE = -1.48128e-05 e
Info: MASS DENSITY = 1.00973 g/cm^3
Info: ATOM DENSITY = 0.0991208 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 30.2467 s, 156.332 MB of memory in use
Info: Startup phase 0 took 0.00019908 s, 156.332 MB of memory in use

-- 
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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
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