[gmx-users] CG-MD simulation of protein, always crash with protein
Trang
ttdtrang at gmail.com
Tue Apr 20 07:13:29 CEST 2010
On Mon, Apr 19, 2010 at 4:08 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> 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.
>
> I made all the modifications suggested, but the system still crashed (with
segmentation fault). However, 'elastic bonds' representation that Martti
suggested works and I may need these modifications later. Thanks for being
so patient with my problem.
>
>
> 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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