[gmx-users] a question about gromacs

Mark Abraham mark.abraham at anu.edu.au
Wed Jul 4 03:50:08 CEST 2007

> Hello,
>   I have an urgent question to ask for help.  I have created a new
> molecule by gromacs and one dihedral of this molecule is designed as 120
> degrees. During the simulation, the dihedral varied from 118 to 122
> degrees, and the average is about 120 degrees. I know this is because
> that the dihedral is defined by harmonic potential, but I want to know
> is this precision enough for the simulation. I mean that is the dihedral
> varying from 118 to 122 proper, or should I constrain this dihedral
> changing from 119 to 121?

It's a harmonic potential, so the value will move around the minimum
defined at 120 degrees... it's just like a marble rolling around a bowl
when you shake the bowl. It won't sit in the minimum, but will move around
it. The behaviour you report is totally normal.


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