[gmx-users] g_rms, g_rmsdist, g_rmsf

Michael Brunsteiner mbx0009 at yahoo.com
Mon Apr 5 16:13:01 CEST 2004

--- Arturas <a3arzi at vaidila.vdu.lt> wrote:
> Hello,
> I have some trivial questions here. Guess they are discussed before
> in
> a part. I checked the manual but there is some misunderstanding
> still.
> 1. I need to calculate the distance over all trajectory between two
> atoms. How to do that ? Is there any third party software (graphical
> ?) to manipulate such analysis easy ? I check that 'g_rmsf' and
> 'g_rmsdist' could be useful, but I am not sure...

make an index file (index.ndx) that contains (beneath others) 
two groups each of which contain only one of your two atoms.
then say:
g_traj -n index.ndx -f traj.xtc -ox coord.xvg
choose the two groups, then x,y,z the coords of both
atoms are output into the file coord.xvg
use, e.g., awk to calculate the distance as function of time
from this file. (if you work with windows you can probably
import the file into excel and do it there)
good luck

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