[gmx-users] "comm-mode = Angular" gives error

[Justin Lemkul]

On 8/21/19 10:50 PM, Jorden Cabal wrote:
> Hi Justin,
> Thank you Justin for letting me know. I will definitely consider increasing
> the simulation box.
> Although, I was wondering that what would happen if I take
> comm-mode="Angular" and comm-grps= "molecule_AB !molecule_AB". This setting
> gives a warning which was ignored using -maxwarn option. After running 10
> ns of simulation, the system seems to be stable and very less fluctuations
> are observed upon visualization compared to when I use comm-mode="Linear".
> or nothing.
> What would you suggest? Should I proceed with the first setting?

Angular COM motion removal is physically incorrect for a periodic 
condensed phase system. Subdividing the system into different groups may 
also be inappropriate, but I still don't even know what's in your 
system. My previous advice stands; you can try to override warnings all 
you like, but it's still a really bad idea. Warnings are there to 
prevent users from doing invalid things. Please take that seriously.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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