Hi, I'm having trouble simulating a protein kinase on water. During the simulation, the molecule moves towards the box limits and some residues apear on the other side. Almost like they are interacting with water molecules on different sides of the box. I'm on my third simulation and the problem persists. I've already tried changing the periodic conditions but with no success. Waht are your thoughts on that?
For additional information: Before the dynamics step I performed 4 minimization steps then i did water dynamics and the entire system dynamics. Here is all the ".mdp " files. Sorry in advance for the long email. FIRST MINIMIZATION STEP: title = min_steepest_descent_PR cpp = /lib/cpp define = -DFLEXIBLE -DPOSRES constraints = none integrator = steep ;l-bfgs nsteps = 20000 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 ; emtol = 209.2 emstep = 0.01 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes SECOND MINIMIZATION STEP title = min_steepest_descent cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 20000 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 emtol = 104.6 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes THIRD MINIMIZATION STEP title = min cg cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 20000 nstlist = 10 ns_type = grid nstcgsteep = 100 rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 vdw-type = Cut-off ;Switch rvdw = 1.4 emtol = 41.84 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes FOURTH MINIMIZATION STEP title = min_steepest_descent cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = l-bfgs ;steep nsteps = 20000 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz coulombtype = PME rcoulomb = 1.0 epsilon-r = 1.0 ;1 for CUTOFF, PME and SWITCH and, 54 for REACTIONFIELD vdw-type = Cut-off rvdw = 1.4 emtol = 41.84 emstep = 0.01 ewald_rtol = 1e-5 optimize_fft = yes WATER DYNAMICS title = 500ps_pr_fixo cpp = /lib/cpp define = -DPOSRES integrator = md tinit = 0 dt = 0.002 nsteps = 250000 ; total 500 ps comm-mode = Linear nstcomm = 1 nstxout = 500 nstvout = 20000 nstfout = 20000 nstlog = 1000 nstenergy = 100 nstxtcout = 500 xtc-precision = 1000 energygrps = Protein SOL NA nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 domain-decomposition = no coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 vdw-type = Cut-off rvdw = 1.4 DispCorr = EnerPres optimize_fft = yes Tcoupl = V-rescale ;berendsen tc-grps = Protein Non-protein tau-t = .1 .1 ref-t = 310 310 gen_vel = yes gen_temp = 310 gen_seed = 173529 Pcoupl = berendsen Pcoupltype = Isotropic tau-p = 1 compressibility = 4.5e-5 ref-p = 1 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no Shake-SOR = no shake-tol = 1e-04 lincs-order = 4 lincs-warnangle = 30 morse = no SYSTEM DYNAMICS title = 10 ns cpp = /lib/cpp include = define = integrator = md tinit = 0 ;3000 ->continuar a partir de 3000 ps dt = 0.002 nsteps = 5000000 ;500000 -> Mais 1ns de simulacao comm-mode = Linear nstcomm = 1 nstxout = 50000 ; trr nstvout = 50000 ; velocidades nstfout = 50000 ; forcas nstlog = 1000 nstenergy = 100 nstxtcout = 10000 ; xtc xtc-precision = 1000 energygrps = Protein SOL NA nstlist = 5 ns_type = grid pbc = xyz rlist = 1.0 domain-decomposition = no coulombtype = PME rcoulomb = 1.0 epsilon-r = 1 vdw-type = Cut-off rvdw = 1.4 DispCorr = EnerPres optimize_fft = yes Tcoupl = V-rescale ;berendsen tc-grps = Protein Non-protein tau-t = .1 .1 ref-t = 310 310 gen_vel = no gen_temp = 310 gen_seed = 173529 Pcoupl = berendsen Pcoupltype = Isotropic tau-p = 1 compressibility = 4.5e-5 ref-p = 1 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no Shake-SOR = no shake-tol = 1e-04 lincs-order = 4 lincs-warnangle = 30 morse = no -- 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