[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

[Chih-Ying Lin]

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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