[gmx-users] constrained mdrun about linear rigid molecule ??
Mark.Abraham at anu.edu.au
Thu Jan 12 16:59:40 CET 2012
On 12/01/2012 8:40 PM, Kiwoong Kim wrote:
> 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.
> 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?
> 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.
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