Dear Justin,<br>Hi,<br>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:<font size="2"><span class="mw-headline">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:<br>title = cholera.mdp<br>cpp = /usr/bin/cpp ; the c preprocessor<br>include = -I/usr/share/gromacs/top<br>define = -DFLEXIBLE<br>constraints
= none<br>integrator = steep<br>dt = 0.002<br>nsteps = 10000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1es<br>optimize_fft = yes<br>;<br>; Energy minimization stuff<br>emtol =
1000.0<br>emstep = 0.01<br>--------------------------------------------------------------------------------------------------<br>Wile pr.mdp file istitle = pr.mdp<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002<br>nsteps = 100000<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstlog = 10<br>nstenergy =
10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e5<br>optimize_fft = yes<br>;Berendsen temperature coupling is on<br>Tcoupl = berendsen<br>tau_t =
0.1 0.1 <br>tc-grps = protein non-protein<br>ref_t = 298 298 <br>;Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 20 20<br>compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>;Generate velocities is on at 298 K<br>gen_vel = yes<br>gen_temp = 298<br>gen_seed = 173529<br>#############################################################<br>Waiting for your
reply.<br>Regards,<br>Lal badshah.<br></span></font><p> Send instant messages to your online friends http://uk.messenger.yahoo.com