[gmx-users] some things I am wondering

[zpxu]

I use parameter of my own, in the topological file.[bonds] and [angles]
section.
 > From: "David van der Spoel" <spoel at xray.bmc.uu.se>
 > To: "zpxu" <zp.xu at mf.mpg.de>
 > Cc: <gmx-users at gromacs.org>
 > Sent: Wednesday, August 21, 2002 2:43 PM
> > Subject: Re: [gmx-users] some things I am wondering
> >
> >
> > > On Wed, 2002-08-21 at 13:44, zpxu wrote:
> > > > and I will be very happy if you tell me why.
> > > > 1) in the section [moleculetype], we must specify the value of
> > nrexcl(excluded numbers)
> > > >     In my understanding, non-bond interactions within the number of
> > bonds are excluded.
> > > >     so if using bond+angle+dihedral, nrexcl will be set to be 3, and
if
> > using bond+angle only,
> > > >     I need only set it to be 2, it is right? for the result of 2 and
3
> > are quite different.
> > > This is force field dependent. Some force fields have dihedrals and
non
> > > bonded interactions between 1-4 atoms.
> >            I use Morse bond potential and G96 angle potential, 6-12 L-J
vdw
> > potential.
> >            then I set nrexcl = 2, is here problem?
> Depends on your force field parameters. But if you uase a default ff
> like GROMOS, this will probably explode.
>
> >
> > > > 2) why we must specify the atom number with bond, and angle
interaction
> > in the [bonds] and [angles]
> > > >    section? because in some cases, if the atoms have great
displacement,
> > the bond and angle list
> > > >    have to be updated, and so I guess the GROMACS have the bond list
> > finding function. but why we
> > > >    must specify it at the topological file?
> > > If the atoms move too far apart such that there are no bonds anymore
> > > something else is wrong. It shouldn't happen.
> >             Yes, then new atom will have bond interaction with that
atom,
> > then how about the new bond?
> >
> > >
> > > > thank for answering suck fundamental questions.
> > > --
> > > Groeten, David.
> > >
________________________________________________________________________
> > > Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> > > Husargatan 3, Box 576,  75123 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> > >
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> > >
> >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>