This document describes the research of a group studying molecular physics and modeling using computational methods such as molecular dynamics simulations and quantum mechanics calculations. It discusses several projects involving simulating lipid bilayers containing thousands of atoms using classical force fields, as well as simulating smaller complexes containing tens of atoms using ab initio molecular dynamics. The goal is to study structural properties and molecular interactions, and also to develop classical force field parameters based on results from quantum simulations. Several supercomputers were used for the large-scale classical simulations and smaller quantum simulations.

1. Group of Molecular Physic
and Modeling
Kaline Cou7nho (kaline@if.usp.br)
Ins$tuto de Física, Universidade de São Paulo, São Paulo, SP, Brazil

2. Molecules
in
phospholipid
bilayer
(~70,000
atoms)
Molecules
in
solu:on
or
in
mixtures
(~
3,000
atoms)
Clusters
(~50
atoms)
Theore:cal
methods:
*
Quantum
mechanics
(QM)
*
Molecular
mechanics
(MM)

3. Classical molecular dynamics of lipophilic
nucleoside (UP) bilayer
DaVinci
• 1
node
with
12
cores
•
2
GPUs
NVIDIA
Tesla
M2050
• 178458
atoms,
49886
molecules
• 10
ns/day
(1
fs/step)
• Total
of
30ns
è
4
days
(1
wai:ng)
• GROMOS
force
field
with
Gromacs
4.6.1*
*www.gromacs.org
We
studied
structural
proper:es
of
bilayers
with
different
concentra:ons
of
UP
and
DPPC.

4. Classical molecular dynamics of lipophilic nucleoside
bilayer and adenine
DaVinci
• 1
node
with
12
cores
•
2
GPUs
NVIDIA
Tesla
M2050
• 422262
atoms,
27954
molecules
• 2
ns/day
(2
fs/step)
• Total
of
40ns
è
26
days
(6
wai:ng)
• GROMOS
force
field
with
Gromacs
4.6.1*
We
studied
the
interac:on
of
Adenine
with
the
bilayers
with
different
concentra:ons
of
UP
and
DPPC.

5. Usually
the
force
field
parameters
of
solvents,
amino
acids
and
nucleic
acids,
sugars
and
carbohydrates
are
good
due
to
the
large
amount
of
experimental
(structural)
informa:on.
But,
what
about
solutes
(inhibitors,
sensors,
anesthe:cs,
drugs,
etc.),
which
in
general
the
experimental
informa:on
are
not
available
?
The
bonded
and
Lennard-­‐Jones
(LJ)
parameters
are
considered
transferable
from
other
similar
molecules,
however
atomic
charges
are
calculated
using
quantum
mechanical
of
isolated
molecule.
(QM
⇒
HF/6-­‐31G*
with
MK,
ChelpG
or
RESP)
Agen:on
with
this
procedure,
because
it
does
not
include
polariza:on
!!!!
[ ]
[ ]
∑
⎥
⎥
⎦
⎤
⎢
⎢
⎣
⎡
⎟
⎟
⎠
⎞
⎜
⎜
⎝
⎛
−
⎟
⎟
⎠
⎞
⎜
⎜
⎝
⎛
ε+
∑+
−ϕ+∑+
δ−ϕ+∑+
θ−θ∑+
−∑=
θ
LJ ij
ij
ij
ij
ij
elec ij
ji
improper
torsions
n
o
angles
or
bonds
r
B
r
A
r
qq
)cos(
V
)ncos(
V
)(k
)rr(kU
612
2
2
4
18021
2
1
2
2
1
2
1
r
U(r)
Lennard-­‐Jones
Coulomb
bonded

6. Experimental
data
N
N
(CH2)n
CN
NC
I-
N
N
(CH2)n
CN
CN
+
+
+
+
+ I-
Ab ini7o molecular dynamics of pyridinium iodide
complex (in vacuum)
C3bis(4CP)2+
+2I-­‐
Blue
Gene/P
• 512
cores
(minimum
available)
• 35
atoms,
108
valence
electrons
• ~
1.2
ps/day
(:mestep
of
0.25
fs)
• Total
of
20ps
è
20
days
(4
wai:ng)
• DFT
(PBE)
with
CP2K*
sojware
*www.cp2k.org

7. Ab ini7o molecular dynamics of pyridinium iodide
complex (in solu7on)
C3bis(4CP)+2
+2
I-­‐
+
80
acetonitrile
• 512
cores
• 515
atoms,
1388
valence
electrons
• ~
0.5
ps/day
(0.25
fs/step)
• Total
of
20ps
è
50
days
(10
wai:ng)
• DFT
(PBE)
with
CP2K*
sojware
We
explain
that
although
two
I-­‐
bind
with
the
pyridinium
only
one
I-­‐
par:cipates
of
the
electronic
excita:on.
Blue
Gene/P

8. Structural proper7es of the ab ini7o molecular
dynamics are used to parameterize classical force
fields
Configura:onal
sampling
Time
evolu:on
of
C
·∙
·∙
I
distance
2.86
±
0.27
Å
3.29
±
0.21
Å