[gmx-users] nrexcl 3 or 4 in combination with pairs 1-4

Berk Hess gmx3 at hotmail.com
Fri Feb 29 14:05:49 CET 2008

> Date: Thu, 28 Feb 2008 16:12:32 +0100
> From: lastexile7gr at yahoo.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] nrexcl 3 or 4 in combination with pairs 1-4
> Dear Gromacs users,
> my system has both 1-4 and 1-5 interactions. I list
> all of them in pairs. According to nrexcl definition
> (gmx mail list), "setting nrexcl to 3 or 4 does NOT
> remove LJ-14". Yet, by switching this option from 3 to
> 4 I have a lot of differences not only in the non
> bonded but also in bonded interactions as well. 
> Searching further the forums I came accross :
> Priority of [ pairs ] and nrexcl?, yet it is
> unanswered. 
> Question1:
> If I have both pairs 1-4 and nrexcl 3 that means that
> atoms, three bonds away, have non-bonded AND LJ14
> interaction or ONLY LJ14 interaction?

The naming in Gromacs is a bit confusing.
nrexcl excludes the normal LJ and Coulomb interactions.
LJ-14 refers to the interactions in the pairs, which are in biomolecular
force fields only used for 1-4 interactions.
I guess you would want to set nrexcl=4

> Question2:
> In pairs should I declare the atom indexes only once?
> For example i j is is enough for declaring the 1-4
> interaction between i and j or have I to insert also j
> i? Doing so I get different results.

You just define a pair interaction between atoms i and j.
Adding j-i adds another pair interaction between j and i, which,
since pair interactions are symmetric, is the same adding i-j.
Doubly defined bonded interactions lead to double bonded interactions.


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