[gmx-users] Re: gmx-users Digest, Vol 65, Issue 122

[xiao shijun]

  Thanks for Mark's fast reply, and It really works.
  Then, I have another qusetion about the manual: It seems that the
exclusion just excludes the nonbond potential of LJ interaction, but
Buckingham. If we want to turn off all VDW interaction between some atoms,
the energy monitor group is a nice choice. I have no idea if I got it right.
   And, we can't use LJ and Buckingham in a same system. Unfortunately, I
met a force-field that most of the nonbond interactions were described by
Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in
[defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a result,
a error message read:  *Trying to add LJ (SR) while the default nonbond type
is Buck.ham (SR).  *I don't know whether it could be settled in gromacs.

   Sincerely
 Shijun


> ----------------------------------------------------------------------
>

> Message: 1
> Date: Mon, 21 Sep 2009 06:24:34 +0000 (GMT)
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: who can help me with the force-field?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbcb8a00405b.4ab71c22 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 09/21/09, xiao shijun  <xshijun at gmail.com> wrote:
> >
> >    Mark wrote:
> >        >  xiao shijun wrote:
> >
> > >> Hi everyone,
> > >>     Recently, I met a problem on the force-field. I am doing something
> > >> on the calcium carbonate, and want to simulation it with gromacs.
> > >> The shell model for oxygen has been emploied in my system. When I
> > >> considered the non-boned potential associated with interactions
> between
> > >> atoms
> > >> in the same CO3 group, I only need to take O-O buckingham interaction
> > >> into account, but any electric interaction. How could I realize that
> in
> > >> my .top file.
> > >>     First, I tried to use [pairs] to eliminate electric interaction,
> but
> > >> I can't add the buckingham interaction of O-O because there is no
> > >> buckingham
> > >> options for LJC14. I want to know if anyone of you have such the
> > >> experience. Thanks!!
> >
> >        >Usually you would not define a nonbonded interaction for atoms
> that are
> >        >so close together, since their interaction should be able to be
> modelled
> >        >adequately with the C-O bond and O-C-O angle (and perhaps with
> CHARMM,
> >        >an interaction harmonic the O-O distance as a Urey-Bradley term).
> >
> >    Thanks for Mark's suggestion. But I want to reproduce the simulation
> from the other paper,
> >  The paper describe the force-field that O-O nonbonded interaction in the
> same carbonate should be considered.
> >  In addition to that, I can't use buckingham potential in [pairs], even
> choose funct = 2. I am wondering
> >  if I want to describe 1-4 interaction by Buckingham, what could I do?
> This is one application for setting nrexcl for moleculetypes. You don't
> want exclusions for particles 2 bonds apart, so set this to one. See chapter
> 5.
>
> If that doesn't work, then if the "bonded" interactions are merely harmonic
> distance potentials, then GROMACS permits a form of them that doesn't create
> a bond (bond type 6, IIRC, check chapter 5; or constraint type 2). Thus, the
> automated exclusion mechanism won't be involved, and you can have Buckingham
> O-O so long as you have Buckingham for all other LJ interactions. You will
> need manual exclusions for C-O pairs, I guess.  Thus
>
> [ atomtypes ]
> C #nonbonded parameters go here
>
> O #nonbonded parameters go here
>
> [moleculetype]
> carbonate
>
> [atoms]
> C
> O1
> O2
> O3
>
> [bonds]
> C-O1 # type 6
> C-O2 # type 6
> C-O3 # type 6
>
> [exclusions]
> 1 2
> 1 3
> 1 4
>
> Whether this works may depend on whatever else is in your system, though.
>
> Mark
>
>
>
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