[gmx-users] Variation of distance between 2 CA atoms with time
ghosh.biplab at gmail.com
Tue May 26 14:42:48 CEST 2015
Dear Gromacs Users,
I am new to Gromacs and using Gromacs-5.0.4.
I want to calculate the variation of distance between to
C-alpha atoms in a protein in course of time.
First, I have created a file called: L153_V161.ndx using make_ndx
and the content of the file is:
[ L153 ]
[ V161 ]
Then I was running the following command:
gmx_mpi distance -f protein.xtc -s protein.gro -n L153_V161.ndx -select
'com of group "L153" plus com of group "V161"' -oav
I am not getting the distance L153-V163 as a function of time, rather its
giving me some average distance of L153.
I would appreciate any help to get the correct answer.
Thanks in advance
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