Average structure of the trajectory

User discussions
1

GROMACS version:
GROMACS modification: No

Hi,

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 ?

Regards
Bhagya

2

Why do you need an average structure of 125 molecules? It will be unphysical.

3

we want it for representation purposes. Please help me.

4

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.

5

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

6

If your system reach equilibrium, there shouldn’t be any difference in bulk property and final output would be representable.