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<PRE>>Kateřina Hynštová wrote:
>><I> Dear users,
</I>>><I>
</I>>><I>
</I>>><I>
</I>>><I> I would like to calculate the mean square displacement.
</I>>><I>
</I>>><I> Using the
</I>>><I>
</I>>><I>
</I>>><I>
</I>>><I> g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg
</I>>><I>
</I>>><I>
</I>>><I>
</I>>><I> I get
</I>>><I>
</I>>><I>
</I>>><I>
</I>>><I> Reading file input.tpr, VERSION 3.3.2(single precision)
</I>>><I>
</I>>><I> Reading file input.tpr, VERSION 3.3.2(single precision)
</I>>><I>
</I>>><I> Group 0( C) has 1 elements
</I>>><I>
</I>>><I> There is one group in the index
</I>>><I>
</I>>><I> Reading frame 0 time 0.000
</I>>><I>
</I>>><I>
</I>>><I>
</I>>><EM> The system always freezes here without any warning or error. I have </EM>
>
>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.
</PRE><PRE>The simulated system is a carbon chain of 1000 united atom units. Ive tried both</PRE><PRE>making the system smaller (less units or extracting the trajectory for one unit)</PRE><PRE>and taking very short time of simulation using the flags -b and -e, the system response is still the same </PRE><PRE>(even after the run over weekend) The simulation and all other tools used so far work ok even for much larger systems.</PRE><PRE>Ive also tried the -msd flag in g_analyze tool, I get the msd graph "immediatelly". </PRE><PRE>The system im running the simulation on is currently CPU INTEL Core 2 Quad Q600 (</PRE><PRE>2.4GHz, 8M, 1066MHz), 4x1G DDR2-800 MHz Aeneon BOX. I have also tried to recompile the g_msd tool.</PRE><PRE>Could I be some problem of e.g. memory? I appologize if Im not giving the exact or sufficient information</PRE><PRE>to about the problem, Im the very begginer. Thank you very much for your help.</PRE><PRE>Best regards,</PRE><PRE>Katka</PRE><PRE>
>Otherwise, how big is the system, how long is the trajectory and what
>system are you running on?
>
>Mark
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