[转载]MPI Gromacs

By default the executables of Gromacs and Open-MPI are not linked to the /bin , If you have a multicore processor machine please follow these steps for successful usage of MPI-Gromacs.

For a protein say 4pss32.pdb with energymini.mdp for energy minimization and finalrunrun.mdp for production run. please follow these steps

np = stands for number of processors to be used (Dual core =2, Quad core =4)

Step-1: /opt/Bio/gromacs/bin/pdb2gmx -f 4ps352.pdb -p 4ps352.top -o 4ps352.gro

Step-2: /opt/Bio/gromacs/bin/editconf -f 4ps352.gro -bt cubic -d 0.5 -o box.gro

Step-3: /opt/Bio/gromacs/bin/genbox -cp box.gro -cs spc216.gro -p 4ps352.top
-o solvated.gro

Step-4: /opt/Bio/gromacs/bin/grompp -np 2 -shuffle -sort -f energymini.mdp -p
4ps352.top -c solvated.gro -o em.tpr

Step-5: /opt/openmpi/bin/mpirun -np 2 /opt/Bio/gromacs/bin/mdrun -v -deffnm em

Step-6:/opt/Bio/gromacs/bin/grompp -np 2 -shuffle -sort -f finalrun.mdp -p
4ps352.top -c em.gro -o pr.tpr

Step-7:/opt/openmpi/bin/mpirun -np 2 /opt/Bio/gromacs/bin/mdrun -v -deffnm pr

Energymini.mdp

title = vif-model
cpp = /usr/bin/cpp
define = -DFLEX_SPC
integrator = steep
dt = 0.001 ; ps !
nsteps = 5000
emtol = 10.0
emstep = 0.01
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = Protein
energygrps = Protein SOL
nstlist = 10
ns_type = simple
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 8
ewald_rtol = 1e-5
constraints = hbonds
optimize_fft = yes

Finalrun.mdp

title = 4ps352-vif
cpp = /usr/bin/cpp
define = -DPOSRES
integrator = md
dt = 0.001 ; ps !
nsteps = 2000000 ; total 2 ns
comm_mode = Angular
;nstcomm = 1
nstxout = 1000
nstvout = 1000
;nstfout = 0
nstlog = 10
nstenergy = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
pbc = xyz
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
;fourierspacing = 0.12
;fourier_nx = 0
;fourier_ny = 0
;fourier_nz = 0
;pme_order = 8
;ewald_rtol = 1e-5
;optimize_fft = yes
tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein SOL
ref_t = 300 300
;Pcoupl = berendsen
;Pcoupltype = isotropic
;tau_p = 1.0
;compressibility = 4.5e-5
;ref_p = 1.0
constraints = All-bonds
;gen_vel = yes
;gen_temp = 300.0
;gen_seed = 173529
constraint-algorithm = Lincs
unconstrained-start = no
shake-tol = 0.0001
lincs_iter = 4
lincs-order = 4
lincs-warnangle = 30
;morse = no

PS:These files are just for an example not adviced to be followed as they are.