It is mot likely that your preparation of the system is somehow
corrupted.
The insertion of a protein in a lipid bilayer might easily introduce
strong
forces in the system and thereby result in a crash of your simulation.
It is also possible that your protein topology is not describing your
system
correctly. This no one can tell without knowing how you built your
topology
and for which kind of system.
Note that cycle in the Martini FF (Tyr/Trp/His) use constrains and are
therefore extremely sensible to strong forces in there environment.
I would suggest you get back to the point where you insert your protein
in the bilayer and check very carefully potential bad contact between
the
protein and the lipid. The minimization should go smooth and running
should not be problematic.
XAvier.
On Apr 15, 2010, at 12:49 PM, Trang wrote:
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 . 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 ), the
distribution of water is even worse than the initial state
(picture). 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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