Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules
Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Position restrained MD. The commands are as follows. minim.mdp and pr.mdp are as follows. And outputs are as follows. Any thing wrong? Thank you Lin 1. Energy minimization of the structure (vacuum) pbc=no grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum 2. Periodic boundary conditions editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0 6.0 3. Solvent addition genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro 4. Addition of ions: counter charge and concentration grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL- 5 Energy minimization of the solvated system => Potential Energy went to the very negative number pbc =xyz (minim.mdp) grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated 6 Relaxation of solvent and hydrogen atom positions: Position restrained MD => Simulation Broke grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR ===================================================================================================== minim.mdp ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of Lysozyme (1LW9.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Definea can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol nsteps = 50000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) ================================================================================================= pr.mdp ; VARIOUS PREPROCESSING OPTIONS title = cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.001 nsteps = 5000 nstcomm = 0 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy = 1 nstxtcout = 0 xtc_precision = 1000 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 200 200 ; Pressure coupling Pcoupl = No ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 1735 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 =======================================================================================================
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