Chemistry Reference
In-Depth Information
AMBER
CHARMM
GROMOS
OPL
S
KBFF
2
15
MOH + HOH
Ben + MOH
10
1
5
0
0
2
1
1
0
0
0
0.5
1
1.5
0
0.5
1
1.5
r
(nm)
r
(nm)
8
8
NMA + HOH
Gly + HOH
6
6
4
4
2
2
0
0
1
1
0
0
0
0.5
1
1.5
0
0.5
1
1.5
r
(nm)
r
(nm)
FIGURE 5.4
The center of mass based radial distribution functions (RDF) for five force
fields for the mixtures methanol (MOH) + water (HOH) at
x
MOH
= 0.5, benzene (Ben) +
methanol at
x
Ben
= 0.75,
N
-methylacetamide (NMA) + water at
x
NMA
= 0.1, and 1
m
zwitter-
ionic glycine (
aq
). Please note the different
y
-axis scales. The data represent the average RDF
from 80 to 100 nanoseconds of production simulation after 10 nanoseconds of equilibration.
The RDFs are converged with respect to time.
similarities are evident in the shape of the RDFs for all FFs excluding GROMOS.
However, the height of the first maximum in the RDFs differs among all FFs.
Note that the GROMOS NMA + HOH
g
NMA- NMA
does not tend toward unity due
to the excessive self-aggregation of NMA in this simulation. For the Gly + HOH
system, the solute-solute RDF does not appear to display a similar shape among
the five FFs. This indicates that the Gly-Gly pairing differs substantially between
the FFs, although the FFs do provide the same excluded Gly-Gly distance. The
