GROMACS version: 2021.1
GROMACS modification: No
I used the following two sets of trjconv to process a 1us trajectory, evenly sliced into 20 with 50ns increments (0-50ns, 50-100ns, etc.):
Set 1:
gmx trjconv -s 6o2p.tpr -f 6o2p.xtc -n index.ndx -pbc whole -center -ur compact -o whole.xtc
gmx trjconv -s 6o2p.tpr -f whole.xtc -n index.ndx -pbc nojump -center -o nojump.xtc
gmx trjconv -s 6o2p.tpr -f nojump.xtc -n index.ndx -pbc cluster -center -ur compact -o cluster_50-100ns.gro -b 5e+04 -e 1e+05
Set 2:
gmx trjconv -s 6o2p.tpr -f 6o2p.xtc -n index.ndx -pbc nojump -center -o nojump.xtc
gmx trjconv -s 6o2p.tpr -f nojump.xtc -n index.ndx -pbc cluster -center -ur compact -o cluster_50-100ns.gro -b 5e+04 -e 1e+05
The results from both sets were uploaded to VMD for visualization and look the same. However, after running “pbc wrap -all -centersel “protein” -center com -compound residue”, all the water molecules appear scattered in the box in all previous frames but all of a sudden cling to the protein on the last frame, repeatedly occurred for every section of the sliced trajectory, from both sets of results:
It seems more of a VMD wrapping issue to me, but I’m not certain. Is there a way to wrap the water molecules around the protein using Gromacs? My original intention was just to keep all the “exploding” water molecules into the same box, so I’ve tried to add another step of -pbc atom, but the whole system turned out to appear messed up.