Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein.
Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 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 813 steps, but did not reach the requested Fmax < 10. Potential Energy = -7.5928356e+05 Maximum force = 3.6197971e+02 on atom 1653 Norm of force = 2.6517429e+00 In my eyes this output was okey so I went on with the md. And here I get the error: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated I already read the error page for this error and also the blowing up page but I still do not know what to do now. My .mdp file for the md runs looks like this: define = -DPOSRES integrator = md dt = 0.005 nsteps = 2000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 0 nstenergy = 5 energygrps = Protein Non-Protein nstcalcenergy = 5 nstlist = 10 ns-type = Grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 gen_vel = yes gen_temp = 200.0 gen_seed = 9999 constraints = all-bonds Are here any optinos which can cause the error? Bests, Eva -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
