Hi As I told in my perevious mail, My system consist of a 2-domain protein (Domain A and B), even when I did EM minimization this 2 damain separated.
my em.mpf is: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 40000 constraint_algorithm = shake shake_tol = 0.0001 nstenergy = 10 nstxtcout = 10 nstlist = 5 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff ; emtol = 10.0 emstep = 0.01 Also it is not because of pbc, What do you suggest for solving this, thank you very much for replying. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. _______________________________________________ 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/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/mailing_lists/users.php
