[gmx-users] g msd freeze

[Mark Abraham]

Kateřina Hynštová wrote:
> Dear users,
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>  
> 
> I would like to calculate the mean square displacement.
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> Using the
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>  
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> g_msd -f traj.xtc -s input.tpr  -n index.ndx -o msd.xvg
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>  
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> I get
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> Reading file input.tpr, VERSION 3.3.2(single precision)
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> Reading file input.tpr, VERSION 3.3.2(single precision)
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> Group   0(         C) has             1 elements
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> There is one group in the index
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> Reading frame 0 time 0.000
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>  
> 
> 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