Sarah Witzke wrote:
Hi again,
Thank you very much for your reply Mark. Now, I have a dihedral with the following form:
22 23 24 25 1 0.0 7.47 1
22 23 24 25 1 0.0 3.9 2
22 23 24 25 1 180.0 1.1 3
22 23 24 25 1 0.0 -2.8425 0
Of course the "problematic" multiplicity of 0 just subtracts 5.685 from the
energy. Would it then be OK to simply delete this line? I suppose it would be OK as it
just adds a constant to the energy but I'm not 100% certain if it would give any problems
with the calculation of forces.
Well, the force is just the displacement derivative of the energy, so as
I pointed out earlier, there can't be any effect of this dihedral there.
If you want to check this, write your forces from two runs with and
without this term to the trajectory file and use gmxcheck to compare them.
I suggest just commenting out this dihedral line - deleting gains
nothing and costs you if you want the line later for some other purpose.
Mark
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