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:
- gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol_com -ox position_A.xvg
- gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol_com -nopbc -ox position_A_nopbc.xvg
- gmx trajconv -f nvt.xtc -s nvt.tpr -b 0 -e 3 -tu ns -seltype mol_com -pbc no -ox position_A_pbcno.xvg
- 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.