Nuno Azoia wrote:
Chih-Ying Lin wrote:
Hi
to simulate the gas phase system, before running MD on the gas phase
system
I have to use the "editconf" command.
But, I DO NOT use "genbox" command.
I'm new to Gromacs, but I think that if you do that you will running
simulation in vacuo. Maybe it a good approximation to gas phase, but
if your box is empty it will be a vacuo simulation.
Technically yes, but gases are mostly empty space anyway. I have seen
examples of gas phase simulations where the molecules were separated by
50 nm in the simulation box (Oostenbrink, et al. (2004) J. Comp. Chem.
25: 1656-1676.
-Justin
Right??
thanks
Lin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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