On 12/01/2012 8:40 PM, Kiwoong Kim wrote:
Hi,
I'm not good at handling Gromacs yet.
My question is about virtual interaction.
I'm doing simulation dealing with CO2 which is linear rigid molecule
as you already know.
As pervasively known, I introduced virtual sites.
However, I don't know how to give initial coordinate correctly of
dummy particles.
Let us consider following system.
x1-----d1-----x2
There are two real atom and one dummy particle between them with
appropriate length ratio, a, from x1, and (1-a) from x2.
If I give the coordinates of three particles by the rules of above
statement, i.e., dummy particle between them with appropriate length
ratio, a, from x1, and (1-a) from x2..
Is it correct?
Looks fine.
Isn't there any unstable energy?
Why should there be?
Do I have to run any preceding run before equilibration run??
Otherwise, Is there any other way giving the correct coordinate of
dummy particle ???
I expect you can give it any coordinates you like, and the interaction
any value of a you like. Thereafter, it's in the hands of physics. If
you want something reasonable, then probably choose the coordinates and
the value of a in a consistent way.
Mark
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