[gmx-users] Re: tpr file problem with analysis and merged trajectories

alkasrivastava at iitb.ac.in alkasrivastava at iitb.ac.in
Fri Jul 25 12:44:54 CEST 2008

sorry the mail was not complete and accidentally sent i m sending it again


I am running a simulation for 60 ns but due to power cutt it stopped at
different time intervals and i continued the run with following command

1. tpbconv -s full.tpr -f full.trr -e full.edr -o full_part1.tpr -until 60000

2. nohup mpirun -np 2 mdrun_mpi -v -s full_part1.tpr -e full_part1.edr -c
after_full.gro -o full_part1.trr -x full_part1.xtc -g full_part1.log -nice
19 >& full_part1.job&

In a way i continued till 60 ns in 5 such breaks so now i have

full.tpr full.xtc
full_part1.tpr full_part1.xtc
full_part2.tpr full_part2.xtc
full_part3.tpr full_part3.xtc
full_part4.tpr full_part4.xtc
full_part5.tpr full_part5.xtc (38-60 ns)

Finally i merged all the trajectories using command

trjcat -f   full.xtc full_part1.xtc full_part2.xtc full_part3.xtc
full_part4.xtc full_part5.xtc -o total.xtc

Now for the calculation of radius of gyration the command i have used

g_gyrate -s full.tpr -f total.xtc -o gyrate.xvg

My question is can we use the starting tpr file (full.tpr) along with the
merged trajectory file (total.xtc) to do some analysis like for example
radius of gyration.

because when i am using

g_gyrate -s full_part5.tpr -f full_part5.xtc -o gyrate_part5.xvg

i am getting a different result.

same way if i am using pbc nojump option for converting the trajectories
using different tpr file i am getting different results

trjconv -s full.tpr -f total.xtc -o nojump.xtc -pbc nojump
g_gyrate -s full.tpr -f nojump.xtc -o gyrate.xvg

and then

trjconv -s full_part5.tpr -f full_part5.xtc -o part5_nojump.xtc -pbc nojump
g_gyrate -s full_part5.tpr -f part5_nojump.xtc -o gyrate_part5.xvg

so ideally the part 5 (38 - 60 ns) should be identical in both the graphs
but it not true, both graphs remarkably different.

Is there any possiblity to merge tpr files of all the breaks and then use
that for merged trajectory.

I don't know how to deal with that.
please help me.

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