[gmx-users] constrained mdrun about linear rigid molecule ??
ilmarekw at gmail.com
Thu Jan 12 10:40:13 CET 2012
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
As pervasively known, I introduced virtual sites.
However, I don't know how to give initial coordinate correctly of dummy
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?
Do I have to run any preceding run before equilibration run??
Otherwise, Is there any other way giving the correct coordinate of dummy
Please help me..
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users