[gmx-users] Variation of distance between 2 CA atoms with time

[Biplab Ghosh]

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 ]
2277
[ V161 ]
2394

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


--BG