[gmx-users] UREA + Protein Simulation error.
karan syal
karansyal86 at gmail.com
Tue Sep 22 09:07:13 CEST 2009
Dear David, Thanks for the reply, guess i will do some literature survey and
see if i can find some validated urea parameters.
karan
On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:
> karan syal wrote:
>
>> 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.
>>
>> Don't use the Urea topology that is in the gromacs distribution. It is
> not based on any force field known to man.
>
>>
>> Thanks again,
>>
>> cherrz
>> karan
>>
>>
>> On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
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