GROMACS version: 2021.3
GROMACS modification: No
Hello Gromacs users,
Question:
How do you centre and remove PBC from a equilibration?
Context:
I am trying to simulate double-stranded DNA. I can successfully run an NVT equilibration but when i come to visualize the trajectory I am faced with an unusual trajectory. I have run
gmx trjconv -s nvt.tpr -f nvt.trr -pbc nojump -o nvt_nojump.trr (stripping water from trajectory)
gmx convert-tpr -s nvt.tpr -n index.ndx -o nvt_nowat.tpr
I get this output (see image)
When you look at the PBC box in VMD,
one of the strands is outside the box. Regardless of the order i do them in e.g., pbc nojump then center or center then pbc nojump i get this dissociation effect.
Could anyone advise as to keep both strands within the box and removed PBC?
Forcefield: AMBER99SB-ILDN
Water: TIP3P
Constraints: Used on terminal base pairs.
Regards,
Dan.