> Date: Thu, 28 Feb 2008 16:12:32 +0100
> From: [EMAIL PROTECTED]
> To: [email protected]
> 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.
Indeed.
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.
Berk.
_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
