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 <jalem...@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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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