[gmx-users] CG-MD simulation of protein, always crash with protein
XAvier Periole
x.periole at rug.nl
Mon Apr 19 11:08:50 CEST 2010
Hi,
the rmsd you show is for the protein in vacuum? It goes up to 0.7 nm!
That is a very
large deformation, is it expected? Isn't your protein freezing and all
the kinetic energy
going into translational motion.
there is a few things you could try.
1- First you should increase the rlilst to at least 1.3 but 1.4 would
be better.
2- And/or reduce the nstlist to 5.
You should modify at least one of the two, that will increases the
cost of your simulation
but should make increase energy conservation.
Then you should try a smaller time step 0.020 ps might just remove all
the lincs warnings.
XAvier.
>
>
> On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori <m.j.louhivuori at rug.nl
> > wrote:
> On 15 Apr 2010, at 18:06, Trang wrote:
> My target system is a protein with lipid molecules added randomly
> (using GENBOX). Running MD, I expect to
>
> I hope you're using a larger van der Waals distance (0.24nm or so)
> when inserting the lipids.
>
> I tried 0.3 - 0.5. It looked fine, but didn't work.
>
>
> broke down the problem, that is, to run md simulation for the
> protein molecule only, and in vacuum. Still no improvement. Although
> all the distances in the minimized structure are visually proper,
> the system exploded.
>
> If you can't run the protein even in vacuum, then the problem is
> either in your MD parameters, starting co-ordinates or some simple
> mistake somewhere. Since the .mdp files you posted seem ok, my bet
> is on the starting co-ordinates, just as Xavier proposed.
>
> Could you post the system topology (.top) and the protein topology
> (.itp), so we can rule out any mistakes in those?
>
> The protein topo is too large, so I put it here. http://pastie.org/926617
> Here is the system topology.
>
> ----------------------------
> #include "../martini_v2.1.itp"
> #include "../martini_v2.1_aminoacids.itp"
> #include "11BHSD1.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
>
> [ system ]
> 11BHSD1
>
> [ molecules ]
> 11BHSD1 1
> ----------------------------
>
>
> You should also double check whether you have close contacts between
> some atoms in the protein; e.g. in VMD this is easily done using the
> "dynamic bonds" representation.
>
> -martti-
>
> Minimized structure showed no close contact (with distance cutoff
> 1.6, even to 1.9). Production run stopped at step 175552 (5266.56
> ps) with Segmentation fault, preceeded with a lot of Lincs warnings
> (I set ring_bonds = "constraints"). This is the mdp file, this file
> goes along with the system in vaccuum that crashed. I'm not sure if
> too long simulation time can be the cause. The strange thing is that
> the system seemed to be relatively stable at the time of crash.
> rmds.xvg is below, in case you want to see the graph first-hand.
>
> -------------------------MD---------------------------
> integrator = md
> tinit = 0.0
> dt = 0.030
> nsteps = 900000
> 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
> tau_t = 0.3
> ref_t = 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
> ----------------------------------------------------------
>
> -------------rmsd.xvg-------------------------------
> @ title "RMSD"
> @ xaxis label "Time (ps)"
> @ yaxis label "RMSD (nm)"
> @TYPE xy
> @ subtitle "Protein after lsq fit to Protein"
> 0.0000000 0.0001400
> 150.0000000 0.6150032
> 300.0000000 0.6162945
> 450.0000000 0.6451609
> 600.0000000 0.6317724
> 750.0000000 0.6501579
> 900.0000000 0.6642945
> 1050.0000000 0.6742513
> 1200.0000000 0.6651280
> 1350.0000000 0.6965100
> 1500.0000000 0.6856629
> 1650.0000000 0.7271055
> 1800.0000000 0.7174531
> 1950.0000000 0.7088170
> 2100.0000000 0.7492073
> 2250.0000000 0.7352809
> 2400.0000000 0.7196461
> 2550.0000000 0.7162255
> 2700.0000000 0.7277457
> 2850.0000000 0.7121301
> 3000.0000000 0.7084662
> 3150.0000000 0.7153199
> 3300.0000000 0.7209989
> 3450.0000000 0.7342823
> 3600.0000000 0.7297466
> 3750.0000000 0.7254455
> 3900.0000000 0.7175814
> 4050.0000000 0.7134616
> 4200.0000000 0.7212958
> 4350.0000000 0.7258847
> 4500.0000000 0.7201833
> 4650.0000000 0.7286560
> 4800.0000000 0.7188574
> 4950.0000000 0.7177775
> 5100.0000000 0.7247230
> 5250.0000000 0.7153631
> -----------------------------------------------------------
>
>
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