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,
Hadi
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 04 2018 - 14:00:02 PDT
