[gmx-users] UREA + Protein Simulation error.

[karan syal]

Dear Justin,

Thanks for the reply!

I will surely try minimize the protein in Vacuum and then try adding Urea
again.

Just that i was wondering how will that effect my artifact bonds which are
between Urea and Water, and not at all between any Protein atom and
Urea/Sol?? As i mentioned earlier, these bonds are formed only after
minimization, they are not present before adding 10M urea+water box (No such
bonds in its individual 10M urea+water .gro either ) to protein, they are
neither there in the before minimized protein+10M urea+water system.


Thanks again,

cherrz
karan

On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> karan syal wrote:
>
>> Dear Gromacs users,
>>
>> I am trying to run a urea+protein simulation and encountering a few
>> problems at various stages.
>>
>> I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I
>> started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)
>>
>> I am using this equilibrated box to add to a globular protein of about 250
>> residues using following commands :
>>
>>
>> editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron    (Giving
>> me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea
>> the number of urea above box should add is 2448.)
>>
>> genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro   (*This adds
>> 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to
>> 10M urea box i have solvated with??)*
>>
>>
> No, it shouldn't.  The protein occupies space within that volume, as well.
>
>
>
>> When i try to minimize this using the following em.mdp
>>
>>
>> cpp                 =  /usr/bin/cpp
>> constraints         =  none
>> integrator          =  steep
>> nsteps              =  5000
>> coulombtype = PME
>> pme_order = 4
>> nstlist = 5
>> ns_type = grid
>> rlist               =  1.0
>> rcoulomb            =  1.0
>> rvdw                =  1.0
>> Tcoupl              =  no
>> Pcoupl              =  no
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  100
>> emstep              =  0.01
>>
>>
>> *It gives me the following output*
>>
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.00000e+02
>>   Number of steps    =         5000
>> Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is
>> larger than the 1-4 table size 2.000 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>> t = 0.015 ps: Water molecule starting at atom 34477 can not be settled.
>> Check for bad contacts and/or reduce the timestep.
>> Wrote pdb files with previous and current coordinates
>>
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 100
>>
>> Double precision normally gives you higher accuracy.
>> You might need to increase your constraint accuracy, or turn
>> off constraints alltogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 34 steps,
>> but did not reach the requested Fmax < 100.
>> Potential Energy  = -1.3092671e+22
>> Maximum force     =            inf on atom 12598
>> Norm of force     =            inf
>>
>> gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)
>>
>>
>>
>> /When i look at the file in VMD, the protein is completely out of the box
>> + There are unusual bonds between a lot of UREA and SOL molecules/. ( The
>> unusual bonds are artifcats after minimization which are not there when i
>> initially look at my P48_10Mrea.gro, that is the gro generated after genbox
>> wth -cs as 10M urea)
>>
>>
> "Out of the box" doesn't exist for a periodic system.  The "bonds" you see
> are also *not* generated by Gromacs, but are also just an artefact of
> visualization.  Bonds are not created or broken in molecular mechanics.
>
>  I tried constraining hbonds as well in em.mdp bit to no effect.
>>
>>
>> I used the above em.gro to run a production run, with following pr.mdp
>>
>>
> Don't, it's a waste of time.  Never just plow ahead when something isn't
> working.  There is something unreasonable about the starting structure.  Try
> minimizing the protein in vacuo first, then add your urea and try EM again.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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