[gmx-users] au virtual atom

[Justin Lemkul]

On 9/3/12 2:45 AM, fatemeh ramezani wrote:
>
> Thanks for your response, but
> I've read the manual. What I realized is that, for example, I should consider for every two, three or … atoms, a virtual atom. Here are some questions:
>   1 - Does not important consider which atoms together? or How much is the angle between atoms?
>   2 -Does I need to manually sort atoms and consider for every group a virtual site?

You have yet to really state what the nature of the virtual site(s) is.  A 
virtual site is constructed by the positions of some amount of atoms, and the 
exact geometry of that construction depends upon where the virtual site(s) 
should be.  How many sites do you need?  Where are they in relation to other atoms?

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
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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