[gmx-users] UREA + Protein Simulation error.
David van der Spoel
spoel at xray.bmc.uu.se
Mon Sep 21 17:21:48 CEST 2009
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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