Re: [AMBER] HMR 4fs error.

From: David A Case <>
Date: Mon, 31 Dec 2018 07:49:22 -0500

On Mon, Dec 31, 2018, M RCC wrote:
>After completion of the simulation, I could not able to visualize the
>trajectory in any of the visualizers like VMD, chimera.
>I tried to convert the trajectory into PDB format, Even then the converted
>PDB file is also unusable.

Can you say exactly how you tried to convert to PDB? I assuming you
were using cpptraj, but cannot be sure. Be sure to look closely at the
cpptraj output: it will report any problems (such as corrupted frames,
etc) that it finds.

It doesn't look (based on very limited information) that this problem
has anything to do with the time step or other details of the
simulation. Are you able to visualize other netcdf trajectory files?
Are there any signs of trouble in the mdout file, such as odd energies
or temperatures or pressures?

Basically, we need to know much more about exactly what you tried, and
what the results were. Saying "not able to visualize" or "unusable"
doesn't give us much information to go on.


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Received on Mon Dec 31 2018 - 05:00:02 PST
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