RMSD with trjconv and -pbc no

User discussions
1

Hi All,

My system contains polymers and water. I want to calculate the RMSD of polymer chains after the simulation. For this purpose, I used the following commands.

A i) gmx trjconv -f md01.tpr -f md01.xtc -o md01_nopbc.xtc -pbc nojump
ii) gmx rms -s md01.tpr -f md01_nopbc.xtc -o rmsd_chainA.xvg -n index.ndx -tu ns

Also, I tried with the following command separately (didn’t do any trjconv).

B) gmx rms -s md01.tpr -f md01.xtc -o rmsd_ChainA_2.xvg -n index.ndx -tu ns -pbc no

I removed the pbc conditions in A (using trjconv) and B (using -pbc no) methods (as per my understanding, please correct me if I am wrong). Yet, I got two different graphs for RMSD.

Appreciate your help in understanding this.

Thank you.

Best regards
Amali

2

gmx rms with -pbc no means that you are not taking periodic boundary conditions into account. That would probably work after having run your trjconv command, but not without it.

I think (but cannot promise) that you would get similar results with:

A i) gmx trjconv -f md01.tpr -f md01.xtc -o md01_nopbc.xtc -pbc nojump
ii) gmx rms -s md01.tpr -f md01_nopbc.xtc -o rmsd_chainA.xvg -n index.ndx -tu ns -pbc no

and

B) gmx rms -s md01.tpr -f md01.xtc -o rmsd_ChainA_2.xvg -n index.ndx -tu ns