Hello My equilibration of water around lumiflavin works (I got no error, no warning and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. What does GROMACS mean with "check bad contacts" and what do you think I should fix? System is lumiflavin in water, CHARMM 27 force field, tip3p water model. Here is my mdp file I used before: define = -DPOSRES integrator = md dt = 0.002 emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 coulombtype = pme vdw-type = cut-off rvdw = 1.2 nstxout = 100 nstvout = 100 nstenergy = 100 nstlog = 100 tcoupl = V-rescale tc-grps = ISO SOL tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = no Thanks for helping me Greetings Lara -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
