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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 21 22:49:03 CEST 2007

Hi Zhongqiao Hu,

Actually, the first procedure will give the wrong results. With option
-b the frames up to that point will be skipped. So the first frame
read, at t(b), will have the jumps removed against the reference
structure given. But in 10 ns, a lot may have happened, making the
reference structure used a very bad reference to remove jumps against.
In stead, with the second procedure, each frame will have the jumps
removed against the previous structure, such that the frame at t(b)
will be reset against t(b-1), which is much more likely to be a proper
reference for that point.

I hope this is a bit clear :S Try to think of what -pbc nojump will do
if there's half a box shift between the reference structure and a



On 5/21/07, Hu Zhongqiao <zhongqiao_hu at nus.edu.sg> wrote:
> Hi,
> 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
> nojump
> 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 coordinates.
> 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 conveniently.
> Zhongqiao Hu
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

More information about the gromacs.org_gmx-users mailing list