Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true?
> title = n.pdb > cpp = /lib/cpp > define = -DFLEXIBLE > constraints = none > integrator = steep > dt = 0.002 > nsteps = 40000 > ;constraint_algorithm = shake > ;shake_tol = 0.0001 > ;nstenergy = 10 > ;nstxtcout = 10 > ;nstlist = 5 > ns_type = grid > rlist = 1 > coulombtype = PME > rcoulomb = 1 > rvdw = 1.2 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 6 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Energy minimizing stuff > emtol = 1000.0 > emstep = 0.01 > freezegrps = Protein > freezedim = Y Y Y > comm_mode = None > > 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: > title = n.pdb > cpp = /lib/cpp > define = -DFLEXIBLE > constraints = none > integrator = steep > dt = 0.002 > nsteps = 40000 > ;constraint_algorithm = shake > ;shake_tol = 0.0001 > ;nstenergy = 10 > ;nstxtcout = 10 > ;nstlist = 5 > ns_type = grid > rlist = 1 > coulombtype = PME > rcoulomb = 1 > rvdw = 1.2 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 6 > ewald_rtol = 1e-5 > optimize_fft = yes > ; Energy minimizing stuff > emtol = 1000.0 > emstep = 0.01 > freezegrps = AU AUI AUC > freezedim = Y Y Y Y Y Y Y Y Y > comm_mode = None -- 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
