[gmx-users] CG-MD simulation of protein, always crash with protein
XAvier Periole
x.periole at rug.nl
Thu Apr 15 13:32:41 CEST 2010
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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