Darrell;
If memory serves, there was a paper in the late '80s of a simulation of
monolayer NH3/graphite by William Steele. It reproduced the lattice dimensions
of our experiments, but seemed to over-estimate the corrugation in the binding
energy relative to our diffraction experiments.
Hope this helps,
Paul Rowntree
Dept. of Chemistry, University of Guelph
>
> Darrell Koskinen wrote:
> > Hi Justin,
> > With regard to your comment about using other force fields for my
> > simulation of graphene surrounded by ammonia gas, are referring to
> the
> > force fields for both graphene and ammonia or only to the force
> field
> > for graphene?
> >
>
> The "force field" should be one in the same. The parameters should be
> suitably
> derived using the same scheme as the original work.
>
> > I reviewed my selection of the force field parameters for graphene
> and
> > see that I selected the parameters from the paper by Cornell et al.
>
> > since a paper on deformation of carbon nanotubes ("A structural
> > mechanics approach for the analysis of carbon nanotubes" by Chunyu
> Li,
> > Tsu-Wei Chou in International Journal of Solids and Structures 40
> (2003)
> > 2487�2499) used parameters from the paper by Cornell et al. Is this
>
> > sufficient to justify the use of these parameters? I also thought
> that
> > graphene and ammonia would be considered organic since they are
> > comprised of carbon, nitrogen, and hydrogen, which are all common
> > elements found in organic matter.
> >
>
> If you feel that precedent is sufficient, then I guess go ahead. But
> realize
> that the paper by Cornell et al. refers to parameters suitable for
> simulations
> of proteins and nucleic acids, as well as a few organic functional
> groups.
> Parameterization was based on peptide backbone geometry, as well as
> other
> parameters, likely none of which involved graphene and gaseous ammonia
> (they
> were doing liquid simulations).
>
> > With regard to the parameters for ammonia, is it acceptable to use
> the
> > parameters from the paper by Cornell et al. or do I need to find
> papers
> > specifically related to ammonia gas molecular dynamics simulations?
> >
>
> I would seriously consider finding parameters (if they exist) that
> have been
> derived for use with gas-phase simulations.
>
> > With regard to dihedral selection, I looked at the .top file and see
>
> > that the function type is listed as 3 in the dihedrals section,
> which I
> > believe indicates that my simulation is using a Ryckaert-Bellemans
> > function. It appears to me that if I am using the OPLS force field
> that
> > the Ryckaert-Bellemans dihedral type is automatically selected. I do
> see
> > in the ffoplsaabon.itp file that there is an improper dihedral
> > definition which think I could potentially use in my simulation
> > "improper_Z_CA_X_Y", but how do I cause my simulation to use this
> > definition? Do I need to add the following line to my .top file?
> > "#define improper_Z_CA_X_Y"
> >
>
> No, you would have to use a special dihedrals section, that specifies
> the four
> atoms involved (function type 1), followed by the specification of
> that
> particular improper ("improper_Z_CA_X_Y"). See the manual for more
> details,
> and/or generate a topology for a protein with pdb2gmx with OPLS-AA and
> see how
> they're defined.
>
> > Further, I thought that I could simply modify the appropriate lines
> of
> > the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters
> found
> > in the paper by Cornell et al. so that they will be used in my
> > simulation. Am I correct in my assumption?
> >
>
> Modifying ffoplsaa files to parameters that are not OPLS-AA is
> probably a bad
> choice. If you're dead-set on using these parameters, download the
> ffamber
> ports and use the ffamber94 force field, not some Frankensteined-OPLS.
> Besides,
> all of the parameters in the Cornell paper are in kcal/mol/A^2, which
> will
> require conversion to Gromacs standard units. If you've printed them
> directly
> in your previous attempts, I can guarantee you you're not getting the
> values you
> think you are.
>
> -Justin
>
> > Thanks again for your help.
> >
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