[gmx-users] "VdW radii" of carbons in an unified-atom system
Kyeong Hyunho
h2kyeong at gmail.com
Tue Aug 2 08:36:16 CEST 2011
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
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