[gmx-users] Sigma and epsilon parameters for water and graphene atoms

[Mark Abraham]

Hi,

On Sun, Jul 31, 2016 at 5:21 PM soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Hi
>    In addition to my last query I would like to know whether the sigma
> values reported for CHARMM 27 are in Angstrom or in nm.


GROMACS conventions are in chapter 2 of the manual. Other conventions you
need to find elsewhere.


> Similarly, is the
> epsilon for atoms in kJ/mol or Kcal/mol? As of now, the values that I got
> from the ffnonbonded.itp in CHARMM 27 are 0 for TIP3P water's hydrogen. Is
> it right?


I generally like to find out how my water model works before I submit my
papers. In this case, yes, but Wikipedia or the original literature are
good places to start learning.

Now if I want to report the graphene-water interaction should I
> take the sigma of CA atoms (carbon atoms in graphene) and water hydrogen
> and then find the arithmetic mean? Similarly, the geometric mean would give
> the epsilon?


The description and equations are all in the manual.


> Is there anything wrong with this approach.Furthermore, in
> ffnonbonded.itp lines are written as below.
>
>
> [ atomtypes ]
> ;name   at.num  mass    charge  ptype   sigma   epsilon
> C       6       12.01100        0.51    A       0.356359487256  0.46024
> CA      6       12.01100        -0.115  A       0.355005321205  0.29288
> CC      6       12.01100        0.62    A       0.356359487256  0.29288
> CD      6       12.01100        0.000   A       0.356359487256  0.29288 ;
> partial charge def not found
> CE1     6       12.01100        0.000   A       0.372395664183  0.284512 ;
> partial charge def not found
> CE2     6       12.01100        0.000   A       0.370613866746  0.267776 ;
> partial charge def not found
> CM      6       12.01100        0.000   A       0.374177461619  0.46024 ;
> partial charge def not found
> CP1     6       12.01100        0.02    A       0.405358916754  0.08368
> CP2     6       12.01100        -0.18   A       0.387540942391  0.23012
> CP3     6       12.01100        0.00    A       0.387540942391  0.23012
> CPA     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPB     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPH1    6       12.01100        0.19    A       0.320723538531  0.2092
> CPH2    6       12.01100        0.32    A       0.320723538531  0.2092
> CPM     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPT     6       12.01100        -0.02   A       0.320723538531  0.37656
> CS      6       12.01100        0.000   A       0.391995435982  0.46024 ;
> partial charge def not found
> CST     6       12.01100        0.000   A       0.278494939291  0.242672 ;
> partial charge def not found
> CT1     6       12.01100        0.07    A       0.405358916754  0.08368
> CT2     6       12.01100        -0.18   A       0.387540942391  0.23012
> CT3     6       12.01100        -0.11   A       0.367050271874  0.33472
> CY      6       12.01100        -0.03   A       0.355005321205  0.29288
> CT      6       12.01100        0.000   A       0.405358916754  0.08368 ;
> partial charge def not found
> CT1x    6       12.01100        0.000   A       0.405358916754  0.08368 ;
> partial charge def not found
> CT2x    6       12.01100        0.000   A       0.358141284692  0.234304 ;
> partial charge def not found
> CT3x    6       12.01100        0.000   A       0.363486677001  0.326352 ;
> partial charge def not found
> H       1       1.008000        0.31    A       0.0400013524445 0.192464
>
>
> For atomtype CA does the sigma and epsilon parameters listed above
> correspond to individual CA atoms or is it between a pair?
>

It's an [atomtype] not a [pairtype]. There's only one type named, so even
if the numbers represent a pair of atoms of the same type, I'm sure you can
tell me the arithmetic and geometric means of two identical numbers. ;-)

Mark


>
>
> Thanks and regards,
> Soumadwip Ghosh
> Senior Research Fellow
> IITB
> India
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