Hello everyone.
I didn't understand difference between united atom and all atom force field.
Is it just about Hydrogen and Carbon atoms??
Thanks.
United-atom force fields do not explicitly represent aliphatic hydrogen atoms. All-atom force fields, as the name implies, do. UA force fields reduce the number of degrees of freedom and therefore speed up the calculation, but the effects are rather small and sometimes it is really important to represent all degrees of freedom.
Dear Mohammadreza:
Between hydrogen and carbon exist covalent bond. It is directed in space and saturation. One carbon atom can interact only four hydrogen atoms. In the description of the interaction between two molecules of methane in a vacuum use effective pair potentials (potential Lennard-Jones). To describe the interaction of two molecules of methane in water is used potential of mean force. It takes into account the contribution to the interaction all forces in the solution (methane /methane, water / water, water / methane). This is an example potential of all molecules force field.
Regards.
United-atom force fields do not explicitly represent aliphatic hydrogen atoms. All-atom force fields, as the name implies, do. UA force fields reduce the number of degrees of freedom and therefore speed up the calculation, but the effects are rather small and sometimes it is really important to represent all degrees of freedom.
All atoms provide parameters for every type of atoms including Hydrogen as separate entity. In United-atom, C-H bond is considered as a single entity. Thus Hydrogen aren't treated exclusively as a separate entity unlike All atoms but parameters are calculated for C-H as a combined entity. So it's like you grouped two atoms and made a "pseudo-atom (as a single unit)" and then provided parameters for this pseudo-atom.
As Justin Lemkul said it decreases Deg of Freedom and help simulate faster.
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