[gmx-users] Re: NH3 / graphene

Paul Rowntree rowntree at uoguelph.ca
Tue Jul 28 02:00:37 CEST 2009


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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