[AMBER] RMS is zero

From: Hadi Rahmaninejad <ha.rahmaani.gmail.com>
Date: Tue, 4 Sep 2018 16:34:23 -0400

Hello Ambe Users,

I am calculating rms of a single atom (Methane) in a system. There are some
atoms which I made them fix using "ibelly", but not the methane. When I
visualize methane with vmd it is clearly moving. However, when I am
calculating the rms using cpptraj program, the output is zero. the command
for cpptraj which I used is like below:
trajin 03_equil.nc
reference 02_Heat.rst
rms first out 03.rms :4201.ME

I highly appreciate if you have any suggestion.
Thank you in advance,
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Received on Tue Sep 04 2018 - 14:00:02 PDT
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