[gmx-users] some things I am wondering

zpxu zp.xu at mf.mpg.de
Wed Aug 21 15:02:24 CEST 2002

----- 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?

> > 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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