>Hi! >We have a problem with a protein-ligand-protein simulation. It is a somewhat >large system (approx. 360 amino acid residues with approx. 70 monosaccharides), >that requires a larger box for proper simulation. >We used exclusions (especifically for the problematic atoms) and restrictions >(tested values of 5000, 2000, 1000 - for backbone and for monosaccharides), >both combined and individually, and when they were kept for the entire >simulation, it went just fine. But when these restrictions and exclusions were >removed, the glycan portion, that isnt connected to any of the proteins >explodes. >Any suggestions? > >Thank you in advance,
Hi, We used the gromos43a1 force fied, and the .mdp with minimization parameters with no restraints or exclusions were: title = Yo cpp = /lib/cpp define = -DFLEX constraints = all-bonds integrator = md tinit = 0000 dt = 0.0005 ; ps ! nsteps = 2000000 ; total 00000-1000 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 optimize_fft = yes pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tc-grps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 50 50 50 50 50 50 50 50 ; Energy monitoring energygrps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 100 K. gen_vel = yes gen_temp = 10.0 gen_seed = 173529 This .mdp file works fine without water, but when we include "sol" the simulation explodes, too. The tc-grps in this case are a glycoprotein (protein-1, gli_1, gli_2, gli_3, gli_4 and gli_5) and a secondary protein (protein-2). thank you again, Giovana Bergamini Faculdade de Farmácia Grupo de Bioinformatica Estrutural Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 Prédio 43431, sala 202 CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil tel.: +55 51 3308 7770 http://www.cbiot. ufrgs.br/ bioinfo -------------------------------------------------------------------- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
