Hello, I have simulated amino acid (eg., glycine) with water solvent mixture in gromacs.. my question is .. 1] How can i find out the solvent orientation (angle made) ie.,angle made by water (HOH) with respect to alpha carbon of amino acid (eg., glycine)...?? 2] I have tried with gmx sorient command ..it gives me five outputs..sori, snor, sord, scum, scount. With sori (it gives from solvent orientation - cos theta -1 to 0) and snor (it gives from solvent normal orientation - cos theta 0 to 1) , but with what respect is it giving i am not able to understand...ie theta 1 and theta 2 3] I wanted to calculate the angle formed between water (HOH) and alpha carbon of glycine. but if it consider the .gro file, i can calculate the angle for only the last frame... but i want to calculate the angle for the full frame (tpr/trr). How can i do it sir...Can u kindly help me regarding this.. Since i am referring one of ur research paper - [Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics]. and in other paper - [MONTE CARLO SIMULATION STUDIES OF THE SOLVATION OF IONS. 2. GLYCINE ZWITTERION] they have calculated the cos theta distribution functions...so i wanted to calculate ..
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