Dear Justin, Hi, I want to do MD simulation of cholera toxin A-subunit.I took PDB file and remove other complexes from the protein so it comes to 185 amino acid residues.Through Whatif server I added the missing atoms. I uses oplsaa force field.Added about 11700 water molecules, closed it in cubic box, added 5 sodium ions.Run the energy minimization but it didn't reached the full and output says:Converged to machine precision, but not to the requested precision.The EM value was in negative.Then I do the equilibration and the mentioned errors occured.My EM file is: title = cholera.mdp cpp = /usr/bin/cpp ; the c preprocessor include = -I/usr/share/gromacs/top define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 10000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1es optimize_fft = yes ; ; Energy minimization stuff emtol = 1000.0 emstep = 0.01 -------------------------------------------------------------------------------------------------- Wile pr.mdp file istitle = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 100000 nstcomm = 1 nstxout = 250 nstvout = 1000 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e5 optimize_fft = yes ;Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 298 298 ;Pressure coupling is on Pcoupl = berendsen tau_p = 20 20 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ;Generate velocities is on at 298 K gen_vel = yes gen_temp = 298 gen_seed = 173529 ############################################################# Waiting for your reply. Regards, Lal badshah.
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