[gmx-users] topology defaults directive

David L. Bostick dbostick at physics.unc.edu
Thu Oct 14 19:35:22 CEST 2004

Thank you Berk,

That clears things up a bit.

I'm sorry I missed your first email somehow, but looked at the online
archives and found it. Pertaining to what you said at the end of that

>For atoms in the pairs section first the parameters in the pairs
>section are checked. If non are present, the ones in pairtypes
>are used. If the atom pair is not present there and gen-pairs=yes
>the pairs are generated from the non-bonded parameters using fudgeLJ,
>if gen-pairs=no a warning is generated and zeros are used.

I tried using gen-pairs=yes and generating a pairtypes list for certain 1-4
LJ interactions in a molecule.itp file. I listed the pairtypes directly
below the atomtypes section.  However, grompp complained about
all of the pairtypes in the list, giving

WARNING 1 [file "ffoplsaa_lipidnb.itp", line 737]:
  Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 2 [file "ffoplsaa_lipidnb.itp", line 738]:
  Trying to add LJ-14 while the default nonbond type is LJ (SR)

Perhaps this means that the only choice is to list the interactions under
the pairs section?


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Thu, 14 Oct 2004, Berk Hess wrote:

> >From: "David L. Bostick" <dbostick at physics.unc.edu>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: <gmx-users at gromacs.org>
> >Subject: [gmx-users] topology defaults directive
> >Date: Wed, 13 Oct 2004 17:35:58 -0400 (EDT)
> >
> >
> >Dear all,
> >
> >In ffgmx.itp, the defaults directive confuses me. This file has the
> >following defaults:
> >
> >[ defaults ]
> >; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >   1             1               no              1.0     1.0
> >
> >This confuses me for 2 reasons:
> >
> >1) The manual says that fudgeLJ and fudgeQQ are not
> >taken unless gen-pairs is yes. So, since in this case gen-pairs is no, does
> >this mean that fudgeLJ=fudgeQQ=1.0 doesn't really do anything?
> As I explained in my answer to your previous mail (and contrary to what
> the current manual says) fudgeQQ is always used for all pair interactions.
> In this case fudgeLJ is not used.
> >
> >2) I see that in ffgmxnb.itp [ pairtypes ] are listed for 1-4 LJ
> >interactions. So if in a molecule.itp file, I have
> >
> >[ moleculetype ]
> >; Name   nrexcl
> >molecule     3
> >
> >the 1-4 intramolecular LJ interactions will be given by the [ pairtypes ],
> >but what about the 1-4 coulomb interactions? With nrexcl = 3 and
> >gen-pairs=no, does this mean that the 1-4 coulomb interaction will be
> >completely excluded?
> No.
> nrexcl only pertains to the normal VdW and Coulomb interactions.
> These are excluded up to the third neighbor.
> Normally the moleculetype section of the topology will contain
> a pairs section which lists all the pair interactions explicitly.
> One can use LJ parameters for the pairs which are different from
> the normal LJ parameters. The charges for the pairs are the same
> as the normal ones, but fudgeQQ can be used to scale the interaction.
> If such a pairs section is not present there are no pair interactions.
> Berk.
> _________________________________________________________________
> MSN Search, for accurate results! http://search.msn.nl
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list