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