Date: Mon, 15 Jul 2019 13:32:32 +0200
Hi all,
I work with the system which consists of 128 lipids bilayer and water
molecules. I used the cpptraj to center the whole system using following
commands:
trajin step6.1_equilibration.nc
trajin step6.2_equilibration.nc
trajin step6.3_equilibration.nc
trajin step6.4_equilibration.nc
trajin step6.5_equilibration.nc
trajin step6.6_equilibration.nc
autoimage origin
center :1-128 mass origin
image origin center familiar
In VMD the system itself looks fine, but when I wanted to check the pbc
box, it only partially overlaps with the system (you can see in the
attached file).
Should I somehow change the cpptraj commands?
Thank you in advance for suggestions
Maria
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