CHARMM Development Project
Posted By: lin1209 Group definition for organic molecule - 12/17/20 01:13 PM
I am trying to run some simple liquid simulation for organic molecules using FF that's not charmm.
I wrote a program to convert the topology to rtf for different compounds, I wrote them all in one group, i.e. all atoms for one compound are in the same group regardless of how big that molecule is.
It works fine for small molecules (e.g. methanol, methane) but I think it raised error for bigger molecules such as N,N-diethylethanamine. I got errors like 'Maximum group spatial extent (12A) exceeded'
What's the proper way to break big molecules into multiple groups? Are there any restrictions for a group?
Thanks in advance.
Posted By: rmv Re: Group definition for organic molecule - 12/17/20 02:29 PM
Other than the size restriction, the convention is that each group should have an integer net charge, i.e. the sum over partial charges for the group should be zero, +/- 1, etc.
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