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

[soumadwip ghosh]

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. 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? 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? 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?


Thanks and regards,
Soumadwip Ghosh
Senior Research Fellow
IITB
India