[gmx-users] simulate Gas Phase system

[Justin A. Lemkul]

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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>>   
>
>

-- 
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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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