[gmx-users] CG-MD simulation of protein, always crash with protein

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Dear gmx users,
I'm trying to run some CG-MD with gromacs, using the available Martini FF.
The first run with {lipid + water} is fine. The POPC lipid bilayer is
successfully self-assembled. I then applied Martini FF for system involving
protein.
All the systems I've tried so far could not survive an md run for long
enough. Most of them crashed at the very first step.

I've encountered different types of errors (range checking error,
segmentation fault...) and even hanging of the system, all of which converge
at the same suggestion that the system hasn't been minimized/equilibrated
well enough.

I've tried some tracing back but still cannot figure out where the problem
can be.

* From screen output, I traced back to the atoms on which large force
affect: most of the cases, these atoms belong to the ring of amino acid such
as TRP, TYR. The worst case was that, 2 beads of 1 TRP totally overlap after
minimization!!! The newest trial is related to atom 195 - 196 - 197, which
are beads of the same TYR
residue<http://picasaweb.google.com/lh/photo/RMSyRH801u44-EiSQjK0-A?feat=directlink>.
What kind of problem can cause such a bad minimization?

* From log file after crashed runs, I found the initial temperature is
extremely high (e.g 6.67074e+12 K, etc). A colleague of mine suggest that it
may be due to the high pressure, which in turn caused by unevenly
distributed molecules in the input structure. This seemed to be reasonable,
for after minimization
(picture<http://picasaweb.google.com/lh/photo/bSLh3oSC5VLxwRrmpeMecQ?feat=directlink>),
the distribution of water is even worse than the initial state (
picture<http://picasaweb.google.com/lh/photo/qNEp0_FZdxiO05PqTVBsTw?feat=directlink>).
But, I get stuck and have no idea why minimization can make system so bad.
This is the mdp for the minimization step
-------------------------------MINI-----------------------------------------------
title                    = Martini
cpp                      = /usr/bin/cpp
integrator               = steep
tinit                    = 0.0
dt                       = 0.025
nsteps                   = 500
nstcomm                  = 1
comm-grps        =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 1000
nstxtcout                = 1000
xtc_precision            = 100
xtc-grps                 =
energygrps               =
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2
DispCorr                 = No
tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
gen_temp                 = 320
gen_seed                 = 473529
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 30
------------------------------------------------------------------------------------


and this is for the next step md
------------------------------------MD--------------------------------------
title                    = Martini
cpp                      = /usr/bin/cpp
integrator               = md
tinit                    = 0.0
dt                       = 0.025
nsteps                   = 50000
nstcomm                  = 1
comm-grps        =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 0
nstlog                   = 2000
nstenergy                = 2000
nstxtcout                = 1000
xtc_precision            = 100
xtc-grps                 =
energygrps               =
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.2
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2
DispCorr                 = No
tcoupl                   = Berendsen
tc-grps                  = Protein W
tau_t                    = 0.3 0.3
ref_t                    = 323 323
Pcoupl                   = berendsen
Pcoupltype               = isotropic
tau_p                    = 3.0
compressibility          = 3e-5
ref_p                    = 1.0
gen_vel                  = no
gen_temp                 = 323
gen_seed                 = 666
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 30
------------------------------------------------------------------------------------

I've struggled with this for about 2 weeks and still have no idea of where
to fix the problem. Am I missing something too basic for tutorials to
mention? I'm sorry for being such a newbie. I've tried my best to figure out
the problem before asking for help. Can you give me some suggestions to get
out of this?
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