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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