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Chapter5.txt
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Chapter5.txt
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>showstart [job id]
#!/bin/bash
#PBS -N PE_5C_70MS_1ns
#PBS -j oe
#PBS -l walltime=4:00:00
#PBS -l nodes=2:ppn=2
#PBS -S /bin/bash
#/bin/bash
>module load GROMACS
>module load cuda
>cd $PBS_O_WORKDIR
#need to create personal folder in /scratch/users/.
>pbsdcp -s md1.mdp EtOHMix70_PE5_EM.gro PE_5C.top PE5.itp ethanol.top /scratch/users/gfm12
>cd /scratch/users/gfm12
>NPROCS=`wc -l < $PBS_NODEFILE`
>grompp_mpi -f md1.mdp -c EtOHMix70_PE5_EM.gro -p PE_5C.top -o md1.tpr -maxwarn 7000
>mpiexec -np $NPROCS mdrun_mpi -v -s md1.tpr -o firstmd.trr -c EtOHMix70_PE5_MD1.pdb -g firstmd.log -e firstmd.edr -cpi state.cpt -cpt 30 -maxh 4
>cd $PBS_O_WORKDIR
#PBS -N PE_12C_test.cuda.oakley
#PBS -j oe
#PBS -m abe
#PBS -l nodes=1:ppn=12:gpus=2
#PBS -S /bin/bash
>set -vx
>module load GROMACS/4.6.3
>module swap intel gnu/4.4.5
>module load cuda/5.0.35
>module list
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
>cd $PBS_O_WORKDIR
>pbsdcp -p mdVer.tpr $TMPDIR
# Use TMPDIR for best performance.
>cd $TMPDIR
>mdrun_gnu_gpu -v -s mdVer.tpr -o mdGPUshort.trr -c mdGPUshort.gro -g mdGPUshort.log -e mdGPUshort.edr -maxh .2
>cat mdGPUshort.log
>cp -p * $PBS_O_WORKDIR/
>ls -al
#PBS -N PE14_Mix50EM
#PBS -j oe
#PBS -l walltime=01:00:00
#PBS -l nodes=2:ppn=12
#PBS -S /bin/bash
>set -vx
# loading the modules
>module load fftw3
>module load GROMACS/4.6.3
# copying all files to nodes
>cd $PBS_O_WORKDIR
>pbsdcp em.mdp EtOHMix50_PE14.gro PE_14C.top ethanol.top PE14.itp $TMPDIR
>cd $TMPDIR
# running the molecular dynamics
>grompp -f em.mdp -c EtOHMix50_PE14.gro -p PE_14C.top -o em.tpr -maxwarn 7000
>mpiexec mdrun_mpi -rdd 2.0 -s em.tpr -o EM.trr -c EtOHMix50_PE14_EM.gro -e EM.edr -g EM.log
# copying files back
>pbsdcp -g em.tpr EM.trr EtOHMix50_PE14_EM.gro EM.edr EM.log >$PBS_O_WORKDIR
>ls -al
>cd /fs/lustre/cwr0408/9.5.2013/PE18
>PE18EM=$(qsub -N PE18em em.pbs)
>echo $PE18EM
>PE18MD1=$(qsub -W depend=afterok:$PE18EM -N PE18Cmd1 firstmd.pbs)
>echo $PE18MD1
>PE18MD2=$(qsub -W depend=afterok:$PE18MD1 -N PE18Cmd2 secondmd.pbs)
>echo $PE18MD2
>PE18MD3=$(qsub -W depend=afterok:$PE18MD2 -N PE18Cmd3 thirdmd.pbs)
>echo $PE18MD3
title = FWS
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.001 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
fourierspacing = 0.40
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
A full md MDP file should contain the following elements starting on the first line:
integrator = md
dt = 0.001 ; ps !
nsteps = 8000000 ;
nstcomm = 1
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.1
coulombtype = PME
rcoulomb = 1.1
vdwtype = cut-off
rvdw = 1.1
fourierspacing = 0.4
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; temperature coupling is on
Tcoupl = v-rescale
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
constraints = all-bonds
;constraints = none
; Energy minimizing stuff
;
emtol = 1.0
emstep = 0.01
; VARIOUS PREPROCESSING OPTIONS
title = AdvancedMDP
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0.0
dt = 0.003
;nsteps = 10000000
nsteps = 10000000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 100
; group(s) for center of mass motion removal
comm-grps
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
;bd-fric = 0
;ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible con-straints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 50000
nstvout = 100000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000000
; Output frequency for energies to log file and energy file
nstlog = 100000
nstenergy = 10000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc_precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps = A B
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacu-um)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
;domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulomb_type = User
;rcoulomb_switch = 0
;rcoulomb = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon_r = 1.0
; Method for doing Van der Waals
vdw_type = User
; cut-off lengths
rvdw_switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
;DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
energygrp_table = A B
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; IMPLICIT SOLVENT (for use with Generalized Born elec-trostatics)
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
;tcoupl = no
;tcoupl = Berendsen
tcoupl = v-rescale
; Groups to couple separately
tc-grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.5
ref_t = 503
; Pressure coupling
Pcoupl = Berendsen
;Pcoupl = Berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and refer-ence P (bar)
tau_p = 5.0
compressibility = 2.755e-5
ref_p = 1.01325
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 503
gen_seed = -1
; OPTIONS FOR BONDS
constraints = none
;constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
;constraint-algorithm = Shake
; Do not constrain the start configuration
unconstrained-start = yes
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint cou-pling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded inter-actions are excluded
energygrp_excl =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
constraints = all-bonds
integrator = md
dt = 0.001
nsteps = 16000000
nstcomm = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlist = 100
ns_type = grid
pbc = xyz
;nwall = 2
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.2
fourierspacing = 0.22
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = yes
tau_t = .1 .1
tc-grps = PE6 SOL
ref_t = 293.15 293.15
; Pressure coupling is off
Pcoupl = no
;Pcoupltype = isotropic
;tau_p = 0.5
;compressibility = 4.5e-5
;ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 298.15
gen_seed = 173529
slab geomery = ewald sums
ewald_geometry = 3dc
PBC=xyz