[AMBER] Difference in velocity values between parmed and pytraj

From: Irfan Alibay <irfan.alibay.lists.gmail.com>
Date: Wed, 7 Aug 2019 16:13:12 +0100

Hi all,

I have noticed that on reading a NetCDF restart file, parmed and pytraj
will report different velocity values which are off by a factor of 20.455.

I unfortunately couldn't find a definite answer as to what velocity units
are used in parmed and pytraj respectively. So, as a sanity check, I was
wondering if anyone on-list could confirm that:

parmed reports velocities in Angstroms per ps
pytraj reports velocities in Angstroms per 1/20.455 ps (as per

Many thanks,

Irfan Alibay
Postdoctoral Research Associate
Department of Biochemistry
The University of Oxford
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Received on Wed Aug 07 2019 - 08:30:02 PDT
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