There is different ways to calculate adsorption energy between a protein and a surface. A very first (and crude) aproximation would be to look at the sum of the non-bonded interaction between your two residues. A better way is to calculate the Potential of Mean Force using steered molecular dynamics such as Umbrella Sampling. I hope it helps. Please be more specific about the software, system and FF used in your next message.

There is different ways to calculate adsorption energy between a protein and a surface. A very first (and crude) aproximation would be to look at the sum of the non-bonded interaction between your two residues. A better way is to calculate the Potential of Mean Force using steered molecular dynamics such as Umbrella Sampling. I hope it helps. Please be more specific about the software, system and FF used in your next message.

You can read this paper. Hope you find this article helpful.

http://onlinelibrary.wiley.com/doi/10.1002/jcc.21421/full

Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces

Use NPT ensemble.

Hello.

Please look to this paper. A very easy way to evaluate drug adsorption.

http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp03216d

Do adsorbed drugs onto P-glycoprotein influence its efflux capability?

Regards,

Ricardo

Mrs/Miss Gandhi,

You cannot obtain electronic spectra by MD. Please pay attention to two discussions in this topic along with shown attachments and references allowing you to obtain information about how to compute both EAs and Fs of any molecular systems, including proteins. There is given also, but briefly, what kind of information you have obtained by MD as well:

Discussion 1:

https://www.researchgate.net/post/How_can_I_ca_lculate_fluorescence_spectra_in_solvent_theoretically

Discussion 2:

(http://www.researchgate.net/post/How_can_I_calculate_the_emission_spectra_and_molecular_geometry_in_excited_state_of_organic_and_coordination_complexes_with_the_help_of_Gaussian03

Particularly for proteins, please pay attention to the attachment herein illustrating computational steps using high level quantum chemical calculations. Details about computational approaches in the chemistry, generally, an particularly for analysis of proteins can be found in [Ref. 1]. This literature source is useful, especially to a broad interdisciplinary audience, balancing between formalism of available theories and their application to real both small and large molecular systems, including organic, organometallics, metal-organics and inorganics. In spite of the fact that there is a broad discussion, namely, on proteins. Given that, you shall receive information what kind of data a MD simulation yields about your protein system.

If you have available Gaussian program package, for example, you can even used the shown in "Discussion 2" technical notes about the computational processing with corresponding methods and keywords, allowing you to realize the shown steps in the attachment posted herein. They are exactly for Gaussian.

 Dear Bojidarka B. Ivanova, 

Neha S Gandhi does not ask about absorption of protein but adsorption.

All the best,

Mathieu