Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my em.pdb file and I saw the Sol box is separated from protein and DNA! Could you please help me, what should I do?what part of my set is wrong?
my em.mdp: define = -DFLEXIBLE integrator = cg ; steep nsteps = 4000 nstlist = 1 constraints = none emtol = 100.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 nstcalcenergy = 1.2 ewald_rtol = 1e-05 coulombtype = PME cutoff-scheme = Group ns_type = grid rlist = 1.4 rcoulomb =1.4 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes Sincerely, Malihe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.