[gmx-users] manual for Gromacs 3.0.2 needed

[Zhao Wei]

Hi!

I'm tring to simulate a lipid bilayer system using Gromacs 3.0.2 to study 
the local pressure through the bilayer. Unfortunately, I did not find a 
manual of this version. Has anyone ever used this package? Could you 
please give me some suggestions? For example, how to modify the following 
.mdp file to meet this need:

integrator               = md
nsteps                   = 25000000
nstlist                  = 10
nstxout                  = 5000
nstvout                  = 5000
nstxtcout                = 0
nstlog                   = 100
dt                       = 0.002
constraint_algorithm     = shake
shake_tol                = 0.0001
constraints              = all-bonds
nstenergy                = 5000 
ns_type                  = grid
coulombtype              = pme     
rlist                    = 1.0
rvdw                     = 1.0
rcoulomb                 = 1.0
tcoupl                   = berendsen
tc_grps                  = lipid sol
tau_t                    = 0.1 0.1
ref_t                    = 323 323 

Pcoupl                   = berendsen
Pcoupltype               = semiisotropic
tau_p                    = 1 1
compressibility          = 4.5e-5 4.5e-5
ref_p                    = 1.0 1.0
optimize_fft             = yes  ?

Thanks!





-- 
Best regards
  
              Wei Zhao

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Laboratory of Computational Engineering
Helsinki University of Technology              
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