Hello researchers
I'm trying to develop force field through which minimization code is being implemented.
Conjugation gradient minimization method is used in minimization. minimization code is implemented according to research article in Java.
Now in preprocessing step for minimization, I'm going to allocate gradient vectors to each atom in the molecule to minimize structure.
Minimization is going along the way to decrease the sum of each gradient vector length
I'm stuck in allocating gradient vectors to each atom in the molecule.
In the force field, intra-energy function types are stretching, bending, torsion, stretching-bending, stretching-torsion, and bending-bending.
How should I calculate gradient vectors to each energy function type?
What is your goal - to develop forcefield/forcefield parameters or to develop a code to run minimization? There are plenty of codes used for FF based simulations e.g. Materials Studio, LAMMPS etc. If you are developing a forcefield, there is probably no need to develop a separate code. It is a way better to convert the forcefield parameters into a proper format to be used in an existing code. If you are trying to develop a code - I am not sure if Java is the best choice. Good luck.
Mr. Shin,
Please pay attentiuon on the content of the following papers and the references cited:
1. Evodiamine and rutaecarpine alkaloids as highly selective transient receptor potential vanilloid 1 agonists, International Journal of Biological Macromolecules, 65, 2014, 314-324, Bojidarka Ivanova, Michael Spiteller
2. Quinoxalines as potent selective CRFRs ligands for monitoring and brain diagnostic, Bioorganic Chemistry, 58, 2015, 53-64, Bojidarka Ivanova, Michael Spiteller
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