[gmx-users] Insertion of protein in lipid bilayer

[David]

On Thu, 2005-07-28 at 10:44 -0500, rob yang wrote:
> Hello gmx'ers,
> I've been struggling with setting up md simulations of glycophorin A in POPC 
> environment. I downloaded the make_hole program by Graham Smith and followed 
> the tutorial as best as I could. My 2 layers of membranes fell apart (from 
> looking at the trp file) and after about 130ps I got the following error:
> 
start without pressure scaling.

> -----
> Grid: 17 x 16 x 19 cells
> WARNING: your box is exploding! (ncells = 5168)
> atomic surface: building atom-vertex nn list...
> ----
> 
> So obviously there's some kinda user errors here as I used arbitrary 
> parameters and what not. This is my input files:
> ----
> topology file:
> #include "ffgmx.itp"
> #include "popc.itp"
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> [ molecules ]
> ; name	number
> POPC    39
> SOL     770
> ----
> lipid.mdp file:
> define                   = -DPOSRES
> integrator               = md
> dt                       = 0.002
> nsteps                   = 500000
> nstxout                  = 5000
> nstvout                  = 5000
> nstlog                   = 5000
> nstenergy                = 250
> nstxtcout                = 250
> xtc_grps                 = POPC  SOL
> energygrps               = POPC  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                  = POPC      SOL
> tau_t                    = 0.1  0.1
> ref_t                    = 300  300
> Pcoupl                   = Berendsen
> tau_p                    = 20
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> ;solvent_optimization     = SOL
> constraints              = all-bonds
> ---
> hp.mdp file:
> holetype                 = MSMS
> hfm                      = 10
> supf                     = 20
> molsurf_log              = gsurf.log
> hz			 = -2.61
> hp1 			 = 1
> hp2 			 = 2028
> s1 			 = 2029
> s2			 = 4338
> hz1 			 = -26.28
> hz2 			 = 26.43
> sfm 			 = 10.0
> sofs			 = 0.15
> molsurf_file             = ./gpa1_msms
> debugsurf 		 = no
> resforces  		 = yes
> 
> I don't want to re-invent the wheels here since I am only trying to learn 
> the protocol so that I can apply it to other membrane proteins later. So if 
> anybody has done simulations using the make_hole program and wouldn't mind 
> posting sample parameter files (.top, .mdp, etc) or sample system with 
> results (bible for us newbies), I would really appreciate it.
> 
> Thank you very much in advance.
> 
> Rob
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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