Re: [gmx-users] g msd freeze

[Justin A. Lemkul]

Quoting Kateøina Hyn¹tová <[EMAIL PROTECTED]>:
> 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?

-Justin

> >Otherwise, how big is the system, how long is the trajectory and what
> >system are you running on?
> >
> >Mark
>
> _
> Explore the seven wonders of the world
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] g msd freeze

[Mark Abraham]

Kateřina Hynštová wrote:

Dear users,

 


I would like to calculate the mean square displacement.

Using the

 


g_msd -f traj.xtc -s input.tpr  -n index.ndx -o msd.xvg

 


I get

 


Reading file input.tpr, VERSION 3.3.2(single precision)

Reading file input.tpr, VERSION 3.3.2(single precision)

Group   0( C) has 1 elements

There is one group in the index

Reading frame 0 time 0.000

 

The system always freezes here without any warning or error. I have 


If your simulation is long and/or computer slow, then it's possible the 
calculation is still running. If so, you can experiment with the -b, -e, 
and -dt flags to make the calculation shorter. See g_msd -h. You can 
also use other analysis tools to check if the problem is localised or not.


Otherwise, how big is the system, how long is the trajectory and what 
system are you running on?


Mark
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