Post on 15-Aug-2015
Group of Molecular Physic and Modeling
Kaline Cou7nho (kaline@if.usp.br)
Ins$tuto de Física, Universidade de São Paulo, São Paulo, SP, Brazil
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)
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.
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.
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
ijij
elec ij
ji
improper
torsions
n
oangles
orbonds
rB
rA
rqq
)cos(V
)ncos(V
)(k
)rr(kU
612
2
2
4
180212
12
2121
r
U(r)
Lennard-‐Jones
Coulomb
bonded
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
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