[gmx-users] constrained mdrun about linear rigid molecule ??

[Kiwoong Kim]

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? Isn't there any unstable energy?

Do I have to run any preceding run before equilibration run??
Otherwise, Is there any other way giving the correct coordinate of dummy
particle ???

Please help me..
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