[gmx-users] readxtc can not get coordinates without jump?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon May 21 06:20:29 CEST 2007

I faced one problem when reading xtc file.
Assuming my xtc file is run.xtc and the last frame no. is 10000 (time
step=1ps, e.g, 10 ns in total), I want to see the coordinates of the
whole system without jump at frame=10000, and I used the command:
(1)trjconv -f run.xtc -s run.tpr -o sys_10000.pdb -b 10000 -e 10000 -pbc
That is no problem, of course.
But I thought I could also do the same thing by 2 steps as follows:
(2.1)  first convert run.xtc to run_nojump.xtc (using -pbc nojump)
trjconv -f run.xtc  -s run.tpr -o run_nojump.xtc -pbc nojump
(2.2) use trjconv again to extract coordinates of system at frame=10000
from run_nojump.xtc ( I thought I didnt need to use flag -pbc nojump in
this case)
trjconv -f run_nojump.xtc -s run.tpr -o sys_10000.pdb -b 10000 -e 10000
But it is strange that some coordinates by 2 ways are different. It
seems that something wrong happened in step2.2 by checking the
But when I add flag -pbc nojump for the step 2.2
trjconv -f run_nojump.xtc -s run.tpr -o sys_10000.pdb -b 10000 -e 10000
-pbc nojump
It does work.
Did anyone meet the same problem and give a reasonable explanation? 
In fact, I want to read coordinates of some particles without jump to
get the Mean Square Displacement (MSD). I used readxtc, a Fortran Code,
to get it, by linking xdr library, which is suggested by Gromacs
developers. But when readxtc read run_nojump.xtc, it can not give the
correct coordinates without jump, similar to what I said above. Then any
method to make a suitable xtc file which allow readxtc to get out
coordinates without jumps? Or after first coordinates with jump are read
out using readxtc, how can I convert them into those without jump in my
Fortran code?
By the way, I need to extract coordinates of some particles satisfying
some specific conditions and these particle changes from one frame to
another frame, so some availabe analysis commands cannot do this
Zhongqiao Hu
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