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Background  Rice ( Oryza sativa  L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE plays an important role in plant photosynthesis, which has been a subject of many studies. Till now, the recognition mechanism between PsaC and PsaD in rice is still not fully understood.    Results  Here, we present the interaction features of  Os PsaC and  Os PsaD by molecular dynamics simulations and bioinformatics. Firstly, we identified interacting residues in the  Os PsaC- Os PsaD complex during simulations. Significantly, important hydrogen bonds were observed in residue pairs R19-E103, D47-K62, R53-E63, Y81-R20, Y81-R61 and L26-V105. Free energy calculations suggested two salt bridges R19-E103 and D47-K62 were essential to maintain the  Os PsaC- Os PsaD interaction. Supportively, electrostatic potentials surfaces of  Os PsaD exhibited electrostatic attraction helped to stabilize the residue pairs R19-E103 and D47-K62. In particular, the importance of R19 was further verified by two 500 ns CG-MD simulations. Secondly, this study compared the stromal ridge complex in rice with that in other organisms. Notably, alignments of amino acids showed these two salt bridges R19-E103 and D47-K62 also existed in other organisms. Electrostatic potentials surfaces and X-ray structural analysis strongly suggested the stromal ridge complex in other organisms adopted a similar and general recognition mechanism.    Conclusions  These results together provided structure basis and dynamics behavior to understand recognition and assembly of the stromal ridge complex in rice.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-016-0877-0) contains supplementary material, which is available to authorized users.

Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.)