[gmx-users] remove the jumps over the boundaries

Milan Melichercik melichercik at nh.cas.cz
Wed Aug 9 15:05:50 CEST 2017

The message says you have used older Gromacs for analysis than was the tpr file was created with. For 2016.x versions you have to use "gmx trjconv" instead of plain trjconv. The trjconv you have called is probably from your Linux distribution and in old version - you can find its binary file using "which trjconv"‎.
BTW why do you store the output to odb file? Cause it will be huge. You should extract only one frame (starting/final) using -dump and than the whole trajectory to xtc file (sure you can use -dt switch or you can skip frames in VMD during the load of xtc file).



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  Original Message  
From: ‪farial tavakoli‬ ‪
Sent: streda, 9. augusta 2017 14:18
To: Discussion List for GROMACS Users
Reply To: gmx-users at gromacs.org
Subject: [gmx-users] remove the jumps over the boundaries

Dear GROMACS users
I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD , it has pbc problem, so I issued this command:
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10
but faced to this error:
Fatal error:
reading tpx file (md_0_1.tpr) version 110 with version 83 program

is anybody help me to solve this problem?
thanks in advanceFarial
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