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
--
========================================
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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