[gmx-users] question about energy minimization

Amit Choubey kgp.amit at gmail.com
Tue Sep 29 10:32:59 CEST 2009

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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