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??)* 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) 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 cpp = /usr/bin/cpp define = -DPOSRES constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 100000 ; total 200 ps nstcomm = 1 nstxtcout = 50 ; collect data every 1 ps nstxout = 100 nstvout = 100 nstfout = 100 nstlog = 100 nstenergy = 100 nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = V-rescale tau_t = 0.1 0.1 ; use items in bold if you have Cl ions tcgrps = Protein Non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 *the simulation stops after following error* t = 0.002 ps: Water molecule starting at atom 36943 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Can anyone pls suggest what should i modify to effectively simulate my system? Any suggestions regarding how i can run a urea+protein simulation with the exact desired concentration will be highly appreciated. Thanks for all the time and pateince, Regards Karan
_______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
