Hello,
at the moment I try to simulate a 50 mer Polyacrylic Acid chain which is half deprotonated using the Gromos53a6 Force Field as a united atom model as MD simulations with Gromacs (no Coarse Graining).
On the included picture, the force field parameters are shown.
My question is now:
Are there the dihedrals between CH2-CH-C=O missing?
Because in my understanding and sense, there is also an dihedral angle between the double bonded oxygen of the carboxyl group or do I miss understand something?
Do you mean in your topology file the dihedral angle missing? Because in this article as you have mentioned there is a dihedral angle definition at CH2-CH-C-O (carboxylate) with 1.00,0,6 parameters.
@Aysegul Turupcu
Yes, I mean if the CH2-CH-C=O angle is missing?
Or should the values be the same.
The paper where I have the values from is not mine.
I can not read from the screenshot which paper you are using. But if this is the paper that you would like to follow or reproduce then you can adapt the parameters if they have also used 53A6 forcefield as well. Otherwise, you can also use ATB program (https://atb.uq.edu.au/) which is an automated topology builder. It will generate building block compatible with GROMOS forcefield also produce output appropriate for GROMACS simulation.
Without being totally familiar with that paper, it seems that they've given you exactly what you need, and that the dihedral for CH2-CH-C-O is the same regardless of whether the carboxyl group is protonated or deprotonated. They're just not using "=" to denote a double bond (because, formally, in a carboxylate, the two resonance forms are equivalent and there is not a discrete double bond).
Of course, this is all really a question for the corresponding author of the paper, who will know all the details, not the RG community, who didn't publish it :)
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