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

Vitaly Chaban chaban at univer.kharkov.ua
Tue Aug 5 09:37:58 CEST 2008

2008/8/5 David van der Spoel <spoel at xray.bmc.uu.se>:
> Vitaly Chaban wrote:
>> Hi,
>> 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.
>> Thanks.
> This is typically low memory. The program reads in principle the whole
> trajectory in memory. You could do the analysis on half of the molecules at
>  a time and average in xmgrace.

Thanks for a clarification. The easy script could solve the problem.

> What is a task manager?  On unix systems you could check the "limit"
> command.

I mean xfce4-taskmanager provided with Ubuntu.

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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