[gmx-users] RE: Insertion of protein in lipid bilayer

[rob yang]

Thanks Graham,
I did follow the position restraint step in my run by restricting P8 in the 
z direction. What happened was that the 2 popc layers flipped right off the 
bat in the md so that the head groups and water from each layer were facing 
each other while the hydrophobic tails from each layer were situated as far 
away from each other as possible. It was really quite bizzare and after 
getting a few chuckles from it, I'd like to find out what I did wrong. This 
is what I did:
1) got the 128 popc pdb and itp from Sir Tieleman, used 
http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar.gz 
forcefields

2) followed the how-to html to create holes using msms.
A few questions here:
a) should I minimize the new membrane with hole?
b) how critical is removing all the possible lipids that may clash with the 
protein?
c) I simply used vmd to manually put my proteins into the membrane lipid and 
saved the coordinate of the protein in a seperate file. Then I copied and 
pasted the simulation box size from the membrane  pdb file to the top of my 
protein file. Is this acceptable? What would be the most bullet-proof 
approach?

3) grompp and mdrun using the following parameters.
run.mdp
---
define                   = -DPOSRES -DFLEX_SPC
integrator               = md
dt                       = 0.002
nsteps                   = 500000
nstxout                  = 5000
nstvout                  = 5000
nstlog                   = 5000
nstenergy                = 250
nstxtcout                = 250
xtc_grps                 = POP  SOL
energygrps               = POP  SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 0.9
vdw-type		 = Cut-off
tcoupl                   = Berendsen
tc-grps                  = POP  SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 10
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
;solvent_optimization     = SOL
constraints              = all-bonds
---
A few questions here too:
a) what would typical values be for the tau_p and tau_t?

4) I havn't got to this step yet but after the hole has been generated 
successfully generated in the membrane, do I append the protein.pdb file to 
the end of the membrane_hole.pdb file and run a normal em/md to the system?

thanks alot.

rob