[gmx-users] au virtual atom
jalemkul at vt.edu
Mon Sep 3 12:07:30 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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