[gmx-users] Insertion of protein in lipid bilayer

[rob yang]

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:

-----
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