I have the topology file for a polymer, i.e. I know all the bonded and non-bonded interaction parameters, but I am unaware of the well-accepted methodology to generate the initial structure. I can think of three methods, to perform this but I am not sure which is the best, or if there are better methods out there.
Method 1: I generate a random initial structure and I do an energy minimization in vacuum (the polymer will shrink in size) and then energy minimization in water (the polymer will grow in size). (I may get stuck in local minima)
Method 2: Use Method 1, then perform Monte-Carlo simulations to find global minima.
Method 3: Use Method 1, then increase the temperature and the reduce to temperature so that I can sample the global minima.
What algorithms does a software like Schrodinger use to find the 3-d structure of the molecule from the chemical formula?
My intention is to develop a python script to do the same work that Schrodinger does, but I can't seem to find a book/paper to do which discusses the available algorithms.
PS: I use GROMACS simulation package.
Method #1 is just fine. There is no rationale in using global minimum as a starting point for a simulation, especially that, for a large polymer, finding the global minimum may take hundreds of years.
Hi Subhamoy,
The method #1 seems more appropriate, maybe if you add a short phase of equilibration it would generate a better initial structure.
Dear Subhamoy Mahajan ,
The method 1 is the one mostly used and the most 'efficient'. To be more sure of your structure, you can creat a simulation box with your polymer and run some MD runs at room temperature for example. After that you can compare the density (or other parameters) of your polymer to the real data that you can find in literature. If the data match, that means that your structure is good (and your potential eventually is good).
Best regards,
Joseph
Answer by Dmitri is the relevant one. What are you trying to study, I guess using atomistic MD? The choice of the structure depends on what you want to study and what system you want to study. For example, if it is simple polymer like poly ethylene, and you want to study quantities such as radius of gyration and so on , then you can start with a random one. If on the other hand, it is protein with definite native conformation, then you better start with the native structure, which should mostly be available in the pdb database.
if its a homopolymer or semirandom copolymer (not something of a very specific 3D structure like a protein) guess whether it's a coil-like or globular one. If it's a coil use something like a random walk to generate the initial structure and minimize with steepest descent to nearest local minimum. If it's a globule, things are a bit harder, but you can generate a walk in a finite sphere, for example and then minimize in vacuum. C-G transitions in atomistic MD can take a while, so it's better to guess beforehand and generate a correct type. Global minima of energy are misleading. For almost any polymer solution (even in a good solvent) the global minimum of configurational energy is a globule, while in reality it might be a coil. Entropic contributions matter a lot in polymer solutions
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