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Group  of  Molecular  Physic    
and  Modeling  
  
Kaline  Cou7nho  (kaline@if.usp.br)  
  
Ins$tuto  de  Física,  Univer...
Molecules	
  in	
  phospholipid	
  bilayer	
  (~70,000	
  atoms)	
  
Molecules	
  in	
  solu:on	
  or	
  in	
  mixtures	
 ...
Classical  molecular  dynamics  of  lipophilic  
nucleoside  (UP)  bilayer
DaVinci	
  
•  1	
  node	
  with	
  12	
  cores...
Classical  molecular  dynamics  of  lipophilic  nucleoside  
bilayer  and  adenine
DaVinci	
  
•  1	
  node	
  with	
  12	...
Usually	
  the	
  force	
  field	
  parameters	
  of	
  
solvents,	
  amino	
  acids	
  and	
  nucleic	
  acids,	
  
sugars...
Experimental	
  data	
  
N
N
(CH2)n
CN
NC
I-
N
N
(CH2)n
CN
CN
+
+
+
+
+ I-
Ab  ini7o  molecular  dynamics  of  pyridinium ...
Ab  ini7o  molecular  dynamics  of  pyridinium  iodide  
complex  (in  solu7on)
C3bis(4CP)+2	
  +2	
  I-­‐	
  +	
  80	
  a...
Structural  proper7es  of  the  ab  ini7o  molecular  
dynamics  are  used  to  parameterize  classical  force  
fields  
C...
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“Simulations of Lipidic Bilayers”. Prof. Dr. Kaline Coutinho – IF/USP.

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“Simulations of Lipidic Bilayers", presented at http://3whpc.lcca.usp.br

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“Simulations of Lipidic Bilayers”. Prof. Dr. Kaline Coutinho – IF/USP.

  1. 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. 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. 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. 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. 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. 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. 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. 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    

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