To get position of my molecule without pbc

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1

GROMACS version:
GROMACS modification: Yes/No
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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.

2

Hi,
gmx trajconv is not a standard gromacs tools
Do you mean
gmx trjconv or gmx traj.?

Maybe gmx trajectory can also be useful.

Best regards
Alessandra

3

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.