Better way to fix the atom -Reg

From: Mani Kandan (
Date: Fri Jun 22 2018 - 10:51:57 CDT

Dear all,

        I want to fix group of atoms during my entire simulation. I tried
to apply harmonic restraints to bind the atoms but it moves slightly. Since
I am applying charges on that atom so I want to freeze that atom in that
position. I can do it by fix atom comment. But I have few questions.

                        1. Which one of the above method is better? and if
I freeze the atom by fix atom comment then what about electrostatics
whether that atom is included or not?

                         2. If I am running NPT simulation then freezing
atom by fix atom comment will affect or not?

                         3. If I am applying harmonic constraints what is
the minimum value to hold its position for silicon nitride?

                         4. Do I want to include all atoms for
electrostatics calculation then What is the better way to fix the atom?

Thanks and Regards,


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