[gmx-users] some things I am wondering
David van der Spoel
spoel at xray.bmc.uu.se
Wed Aug 21 15:08:49 CEST 2002
On Wed, 2002-08-21 at 15:02, zpxu wrote:
> ----- Original Message -----
> 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
> 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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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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