[gmx-users] re: Self-assembly simulation of lipids

[Alif M Latif]

Dear GROMACS users,
   
  Thanks for all the replies. They're very helpful. Actually, i have no expertise in this field around me. Moreover i'm from chemistry, so statistical and quantum mechanics are no familiar to me. Thats made my progress become slower (but not impossible right?). 
   
  I have done several simualtions using the .mdp file that i modify from the example included in the online manual. I'm using the OPLS-AA force field with the reason i'm doing liquid simulations. I have succeeded in doing some simulations (as a practice), got some problems and i solved it most based on these helpful mailing-lists. Its just that i wan to make sure what i'm doing is right until now. 
   
  I am doing MD simulation on the mixture of Oleyl oleate (palm oil ester) / Sorbitan Monolaurate (Surfactant) in water. The composition is based on experimental results. I packed these molecules using Packmol (excluding water).I added water molecules using genbox in calculated box size. After conjugated-gradients and steepest descents energy minimizations, i run MD simulation.
   
  Here's my .mdp file.. any comments and suggestions are very welcomed and helpful.
   
    title                              = MICELLE #7
  cpp                              = cpp
  include                         = -I/usr/local/gromacs/share/gromacs/top
  define                           = 
  integrator                      = md
  dt                                 = 0.001
  nsteps                          = 5000000
  emtol                            = 50.0
  emstep                         = 0.01
  niter                              = 20
  nstcgsteep                    = 1000
  nbfgscorr                       = 10
  nstxout                          = 50000
  nstvout                          = 50000
  nstlog                           = 5000
  nstenergy                      = 250
  nstxtcout                       = 250
  xtc-precision                  = 1000
  xtc_grps                        = System
  energygrps                    = System
  nstlist                            = 10
  ns_type                         = grid
  pbc                               = xyz 
  rlist                               = 0.8
  coulombtype                  = cut-off
  rcoulomb                       = 1.2
  vdw-type                        = Cut-off 
  rvdw                              = 0.8
  table-extension              = 10.0
  pme_order                     = 4
  ewald_rtol                      = 1e-05
  tcoupl                           = Berendsen
  tc-grps                          = System
  tau_t                             = 0.1
  ref_t                              = 298 
  Pcoupl                          = Berendsen
  pcoupltype                    = isotropic
  tau_p                            = 1.0
  compressibility              = 4.5e-5
  ref_p                             = 1.01325
  gen_vel                         = yes
  gen_temp                      = 298
  gen_seed                      = 173529
  constraints                    = none
 
Thank You for reading.

-------------------------------------------------------------------------------------------------------------------------------------

M. Alif M. Latif
Chemistry Department, Faculty of Science,
Universiti Putra Malaysia,
43400 UPM Serdang, Selangor,
Malaysia


       
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