It is often necessary to know the parameters of Lennard-Jones (LJ) potential for various atoms. There may be database for LJ parameters. I am just curious to know how these parameters are obtained from experimental data or using ab initio computational methods.
Dear Uttam,
Please see my paper. You can find full text in researchgate also.
Lennard-Jones Energy Parameter for Pure Fluids from Scaled Particle Theory
Reza Tahery · Hamid Modarress
Jun 2007 · IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING
See http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199802)19:3%3C334::AID-JCC7%3E3.0.CO;2-U/full?2-U/full for the approach used in CHARMM.
generally it can be done with gromacs using g_energy command in the case of you have a trajectory of dynamics simulation but online there are many tools correlated with references that you can read
Hi Polo. I do not think there is any logic to calculate Lennard-Jones parameters from the trajectory or energy files. If you know the interaction parameters, only then you can calculate trajectory or energy of the system. What I mean is that you need to collect LJ parameters first. After that you can solve equations of motion to obtain trajectory.
im refers to the trajectory of your protein after molecular dynamics simulation a certain ns time step.no the energies files. it is logical to calculate because the motions of structure of protein is due to the sum of all the forcies around the protein that can influence the final structure position in the space. perhaps i have misinterpreted your questions!
That is the point of the question - one cannot do the simulation without the requisite parameters.
Dear Uttam,
Please see my paper. You can find full text in researchgate also.
Lennard-Jones Energy Parameter for Pure Fluids from Scaled Particle Theory
Reza Tahery · Hamid Modarress
Jun 2007 · IRANIAN JOURNAL OF CHEMISTRY & CHEMICAL ENGINEERING
friend, have you found the database for LJ parameters ? i need it too.
TD-DFT is the best method to calculate this here is some articles:
- Marques, M. A. L.; Castro, A.; Malloci, G.; Mulas, G.; Botti, S. Efficient calculation of van der Waals dispersion coefficients with time-dependent density functional theory in real time: Application to polycyclic aromatic hydrocarbons. The Journal of Chemical Physics2007, 127 (1), 014107 DOI: 10.1063/1.2746031.
- Banerjee, A.; Autschbach, J.; Chakrabarti, A. Time-dependent density-functional-theory calculation of the van der Waals coefficient C6C6 of alkali-metal atoms Li, Na, K; alkali-metal dimers Li2LiX2, Na2NaX2, K2KX2; sodium clusters NanNaXn; and fullerene C60CX60. Phys. Rev. A 2008, 78 (3) DOI: 10.1103/PhysRevA.78.032704.
- T. Gould, T. Bucko, J. Chem, Theory Comput. 2016, 12, 3603-3613.
Article C6 Coefficients and Dipole Polarizabilities for All Atoms an...
@ Panpan Zhang if you have Gaussian09 software in it's folder there are some *.prm files. You can find Lennard Jones parameters for almost all elements in these files. Be careful about units you will have to convert units.
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