[gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed

Vitaly Chaban chaban at univer.kharkov.ua
Sat Aug 2 12:57:39 CEST 2008


I calculate the diffusion constants via Green-Kubo relation for a
system of 216 molecules (5 sites in each). The velocities are saved
every 0.005 ps and the total trajectory is 1000 ps long. Then applying
g_velacc -nonormalize -mol -n index.ndx -acflen 1001
The process starts and after some time is killed:

trn version: GMX_trn_file (single precision)
Reading frame  165000 time  825.000   Killed

If one gives a less part of the trajectory:
'g_velacc -nonormalize -mol -n index.ndx -acflen 1001 -b 300 -e 600'
the calculation is OK.

Low memory or what? It doesn't look so according to the task manager.
Has anybody experienced the same problem? Any tricks to overcome it?
Found on version 3.3.1.


Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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