Hi everyone, I recently was doing a simulation where i had inserted water into the system forcefully( using -ci -nmol option of the genbox). I didnt change the box dimensions after the insertion of the extra molecules. Then i did energy minimization on the system and somehow it moved the atoms out of the box (some co-ordinates became negative and some became more than the box size). I did not want the program to do this i would have rather removed some of the molecules. Is there a way to control this? Interestingly, the energy minimization log didnt show any of the above changes, it also didnt change the box size in its output gro file?
I actually didnt realize this until i did a long simulation after which the trajectories of some of the atoms looked way out of the box dimensions. The co-ordinates of many atoms didnt lie in the box range. Although the output file contained the same box dimensions as I started with. Could someone help me in understanding what happened? Thank you, Amit Choubey
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