Tutorial-l Mailing List

From: Greipel.Joachim_at_mh-hannover.de
Date: Thu Jun 28 2012 - 01:25:07 CDT

When running the IMD-Tutorial (alanin.conf) under Linux with NAMD 2.9 the
downloaded binary (2.9, 2012-04-30) for multicore x86_64 without cuda
support is running OK.
 
In contrast using the binary for multicore with cuda support yields a long
list of atom velocities being too fast. NAMD exits prematurely. This is not
really a matter of IMD, since running the simulation non-interactively does
not change the errors:
......
ERROR: Atom 64 velocity is 134811 215975 183254 (limit is 8000, atom 63 of
66 on patch 0 pe 0)
ERROR: Atom 65 velocity is -1.87796e+06 -3.00879e+06 -2.55259e+06 (limit is
8000, atom 64 of 66 on patch 0 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (27 atoms on
patch 0 pe 0).
......
 
System: Linux SLES11SP1/ Dual XEON E5630 / Dual Quadro FX 3800 / Supermicro
Mainboard
 
Anyone knows the reason?
 
Thanks,
 
Joachim
 
 


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