AMBER Archive (2009)

Subject: [AMBER] perform an analysis using ptraj

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Dear All,

I want to perform an analysis using ptraj or other analysis tools in Amber
10 for the subjects I wrote below:

1 To calculate Self-diffusion coefficient

   - Mean square displacements ( MSD )

   - velocity autocorrelation functions

2 To calculate viscosity

      - autocorrelation functions of the stress tensors

I searched Amber manuals, tutorials and mail archive. But I couldn't get an
information about obtaining them. I think that Amber can calculate
Self-diffusion coefficient and viscosity. Could you please give me some
information if Amber can be used to obtain Self-diffusion coefficient and
viscosity ? I'm waiting for the user's help who have some experience 0n
calculating them.

Thank you very much for your attention.

Sincerely
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• Previous message: Jeremy Harris: "[AMBER] amber tools reading netcdf files"
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