[gmx-users] g msd freeze

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 8 11:57:26 CEST 2008

Quoting Kateøina Hyn¹tová <hynstova at hotmail.com>:
> The simulated system is a carbon chain of 1000 united atom units. Ive tried
> bothmaking the system smaller (less units or extracting the trajectory for
> one unit)and taking very short time of simulation using the flags -b and -e,
> the system response is still the same (even after the run over weekend) The
> simulation and all other tools used so far work ok even for much larger
> systems.Ive also tried the -msd flag in g_analyze tool, I get the msd graph
> "immediatelly". The system im running the simulation on is currently CPU
> INTEL Core 2 Quad Q600 (2.4GHz, 8M, 1066MHz), 4x1G DDR2-800 MHz Aeneon BOX. I
> have also tried to recompile the g_msd tool.Could I be some problem of e.g.
> memory? I appologize if Im not giving the exact or sufficient informationto
> about the problem, Im the very begginer. Thank you very much for your
> help.Best regards,Katka

How was your Gromacs version compiled, and what version are you using?  What
version of gcc was used?


> >Otherwise, how big is the system, how long is the trajectory and what
> >system are you running on?
> >
> >Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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