[gmx-users] G53A6, non-symmetric selection metrix

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Fri Dec 11 00:42:59 CET 2015

Dear All,

Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink  *et al.
Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
confused about van der waals interactions between non-bonded atoms.

for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
and these combination rules (eq. 15 in article) make use of selection
matrix (table 8 in article). However this selection matrix is not

This means L-J interactions between two atom types depends to the order we
put them in [pairs]. Is it correct?

If this is true, then the order of atom numbers in [pair] matters. But it
does not make sense, why (Cij 12) should be different from (Cji 12)?

Thanks in advance for your comments


*Rewards work better than punishment ...*

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