Simulacao Bioquimica

Programas

Tutoriais

 

To do List

  • Modelos iniciais
  • Construção dos modelos de membranas 
  • Topologias 
  • Steepest descent
  • MD Curta
  • MD de Producao
  • Análise












1.       Modelos iniciais

a.       Popc

b.      Chol

2.       Construção dos modelos de membranas

a.       Ssh

b.      Editconf

c.       Genconf

d.      Nowaters

e.      Xemacs

3.       Topologias

4.       Steepest descent

a.    Ficheiros .mdp

b.      Lamboot/mpirun

c.      Grompp / mdrun

5.       MD curta

6.       MD de producao

7.       Analise

a.       Energia potencial

b.      Area por lípido

c.       Volumes por lipido

d.      Espessura da membrana

e.      Densidade da membrana

f.        RMSD

g.       Localizacao de atomos importantes:

                                                               i.      OH(Chol)

                                                             ii.      P

                                                            iii.      C (fosfolipidos e chol)

h.      Numero de contactos (d<0,7nm)

i.         Pontes de H

j.        SCD

k.       Tilt

                                                               i.      Sn 1

                                                             ii.      Sn 2

                                                            iii.      P-N

                                                           iv.      Chol

l.         MSD

                                                               i.      Popc

                                                             ii.      Chol

m.    Dinamica rotacional

                                                               i.      Sn 1

                                                             ii.      Sn 2

                                                            iii.      P-N

                                                           iv.      Chol

n.      Rdf

                                                               i.      Sn 1 sn 1

                                                             ii.      Sn 1 all

                                                            iii.      Sn 1 sn 2

                                                           iv.      Sn 2 sn 2

                                                             v.      Sn1 all

                                                           vi.      Chol Chol

                                                          vii.      Chol sn 1

                                                        viii.      Chol sn2

o.      H2O order

p.      Potencial electrostatico atraves da membrana