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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