[gmx-users] Re: Largest charge group radii for Van der Waals; Largest

[Justin A. Lemkul]

Tom wrote:
> Thanks for all the replies about my question!
> 
> Justin: you might be right. I continued a simulation after manual re-assembling
> two objects from two simulations. For one object, part of the molecule split
> accross PBC. I combine this object with the other one.
> 
> Is there any way to solve this to avoid any mistake for the continued
> simulation?
> 

In principle, nothing is wrong, as long as the distance grompp is complaining 
about corresponds to one of your box vectors.  Your molecule is split; there is 
no requirement that molecules necessarily be whole in a periodic system.

-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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