# To get position of my molecule without pbc

**URL:** <https://gromacs.bioexcel.eu/t/to-get-position-of-my-molecule-without-pbc/1515>\
**Category:** User discussions\
**Created:** [January 30, 2021, 4:34pm UTC](https://gromacs.bioexcel.eu/t/to-get-position-of-my-molecule-without-pbc/1515 "2021-01-30T16:34:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![RamKrishna](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ramkrishna/32/626_2.png) [@RamKrishna](https://gromacs.bioexcel.eu/u/RamKrishna)\
**Post date:** [January 30, 2021, 4:34pm UTC](https://gromacs.bioexcel.eu/t/to-get-position-of-my-molecule-without-pbc/1515/1 "2021-01-30T16:34:18Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

I had run a simulation of 100 ns including 1 molecule of A and 2000 molecule of B in a box size of 3.931 nm in gromacs 2020.2 with NPT equilibration run and NVT production run with pbc on and generated nvt.xtc file.  
Now I want to generate a file containing position of center of mass of molecule A from initial to 3 ns without pbc (i.e. to find real coordinates of A). And I had tried the following gmx codes in order to generate the same:

1. gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol\_com -ox position\_A.xvg
2. gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol\_com -nopbc -ox position\_A\_nopbc.xvg
3. gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol\_com -pbc no -ox position\_A\_pbcno.xvg
4. gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol\_com -pbc yes -ox position\_A\_pbcyes.xvg

But when I viewed these all 4 xvg files I found no any differences in the coordinates. The pbc effect was unable to nullified by (-nopbc) and (-pbc no) extensions and everytime either x or y or z coordinate reaches near to 3.931nm (box size), the coordinate suddenly jumps around 0 nm in next frame where each coordinate shift after every successive frame is less than about 0.1 nm. I am stuck in this problem.  
Help me to figure out my problem.  
Thanks in advance.

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [February 1, 2021, 9:04pm UTC](https://gromacs.bioexcel.eu/t/to-get-position-of-my-molecule-without-pbc/1515/2 "2021-02-01T21:04:22Z")

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Hi,  
gmx trajconv is not a standard gromacs tools  
Do you mean  
[gmx trjconv](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html) or [gmx traj](https://manual.gromacs.org/current/onlinehelp/gmx-traj.html).?

Maybe [gmx trajectory](https://manual.gromacs.org/current/onlinehelp/gmx-trajectory.html) can also be useful.

Best regards  
Alessandra

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**Author:** ![RamKrishna](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ramkrishna/32/626_2.png) [@RamKrishna](https://gromacs.bioexcel.eu/u/RamKrishna)\
**Post date:** [February 2, 2021, 2:21am UTC](https://gromacs.bioexcel.eu/t/to-get-position-of-my-molecule-without-pbc/1515/3 "2021-02-02T02:21:31Z")

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Oh I am sorry for my mistake. You are right. It is actually ‘trajectory’ not ‘trajconv’. But the other parts and my conditions are same.