Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is:
1. How can one recenter solvent around solute and at the same time keep the original unit shape? I used the following command to get this picture: trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact where for centering the solute was used and the whole system was saved to the output trajectory. Thanks, Dimitar
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