GROMACS modification: No
I need to get an average structure from the multimolecular ( 125 of same short-chain molecules) trajectory? The average structure should be a single molecule. Can someone pls help me on this ?
Why do you need an average structure of 125 molecules? It will be unphysical.
we want it for representation purposes. Please help me.
Maybe just pick one frame that looks representable.
I wonder if you are looking for the molecular geometry at energy minimization.
If that is the case, you just need the output from the energy minimization.
In my system I have 125 identical molecules. I want to see the average structure of that. Need to get an idea about how it’s in bulk system. Please help me
If your system reach equilibrium, there shouldn’t be any difference in bulk property and final output would be representable.