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

[Piggot T.]

Hi Mohsen,

This table can indeed be quite confusing at first. I suggest you take a look at http://redmine.gromacs.org/issues/773#note-10 where there is a discussion of how to interpret table 8 (for a specific example, but it should highlight how it works). Hopefully that should answer your questions.

Cheers

Tom
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mohsen Ramezanpour [ramezanpour.mohsen at gmail.com]
Sent: 10 December 2015 23:42
To: Discussion list for GROMACS users
Subject: [gmx-users] G53A6, non-symmetric selection metrix

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
symmetric.

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

Best,
Mohsen

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