Hello, dear gromacs users, I am trying to get a hint of appropriate values of "VdW raii" of carbons. For this I calculated r_m from gromos53a6. It uses LJ combination rule #1, so to my understanding the ratio of the last two columns in ffnonbonded.itp equals sigma^6. From r_m^6 = 2*sigma^6 I could calculate r_m for each atomtype. Now I'm confused because the calculated values for r_m are smaller for HC than C. Moreover they show a monotone pattern; CH1 > CH2 > CH3 > CH4.
;name, r_m, epsilon C 0.2010 8.8770 CH0 0.3726 0.2239 CH1 0.2817 3.0365 CH2 0.2284 13.1374 CH3 0.2103 27.7488 CH4 0.2082 40.4358 CH2r 0.2220 15.3369 CR1 0.2100 16.0851 HC 0.1332 3.7882 In combination rule #1, the optimal distance of any two atoms is to be calculated as the geometric mean of r_m, isn't it? Then these values indeed roughly translate to sizes. But for instance in phenylalanines, does HC really pack so much closer with other atoms than C does? Many thanks, Hyun-Ho -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
