[gmx-users] Solvating dodecahedron

[Justin A. Lemkul]

Tsjerk Wassenaar wrote:
> Hi Justin,
> 
>> Note that the pseudo-sphere representation is for visualization
>> purposes only; the triclinic cell should be the input for any simulation.
> 
> This not true. It doesn't matter which representation you use as
> input. Molecules may be broken over PBC, but the topological
> information is taken from the .tpr file anyway. Gromacs may spit out
> broken molecules, and will swallow them just as well.
> 

Good to know, and that certainly makes sense.  I guess I was thinking of an old 
post that warned never to do this; perhaps there was some problem with PBC 
handling in an older version, and thus I made a habit to never change the input 
coordinates.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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