[gmx-users] confusion about pdb file and coordinate.xvg file

biki bikramjit_101 at yahoo.com
Mon Feb 4 13:58:36 CET 2013

Hi all,

I am doing simulation of 864 spce water molecules in a cubic box of 3nm
length in gromacs-4.55 version.

I have generated the trajectory file using trjconv utility in gromacs. Using
the  trr file used to generate the .pdb file, I have generated the
co-ordinates of H atoms of water using g_traj utility. I thought I will get
the same value of co-ordinates of H atoms  in both the files in a particular
time step. But it was not so. I am attaching here a part of both the files
containing the co-ordinates of H atoms in the first time step. Please note
that I have modified and removed the co-ordinates of oxygen atoms from the
pdb file. 

My doubts are:
1. Am I wrong in thinking that in both the files, co-ordinates of same atoms
in a particular time step should be same?
2. If I am wrong, then what is correct ?
3. If I am correct then  what may be the possible cause of having different
coordinates in both the files?

Best Regards,

traj.pdb <http://gromacs.5086.n6.nabble.com/file/n5005150/traj.pdb>  
Hcoord.xvg <http://gromacs.5086.n6.nabble.com/file/n5005150/Hcoord.xvg>  

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