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

biki bikramjit_101 at yahoo.com
Mon Feb 4 14:06:45 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. So, Its not exactly the standard format. 

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, 

Hcoord.xvg (57K) <http://gromacs.5086.n6.nabble.com/attachment/5005151/0/Hcoord.xvg>
traj.pdb (167K) <http://gromacs.5086.n6.nabble.com/attachment/5005151/1/traj.pdb>

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