148 lines
3.3 KiB
Bash
Executable File
148 lines
3.3 KiB
Bash
Executable File
#!/bin/bash -l
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usage() { echo "Usage: $0 [-d basedirectory ]" 1>&2; exit 1; }
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DIRECTORY="."
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while getopts "d:" opt; do
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case $opt in
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d )
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DIRECTORY=$OPTARG
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;;
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h )
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usage
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;;
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\? )
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usage
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;;
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esac
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done
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cd $DIRECTORY
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#=====================================================================================
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cat > mdp_parameters.mdp << EOF
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integrator = INTEGRATOR
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dt = 0.001
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nsteps = NSTEPS
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nstcomm = 10
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nstlog = NLOG
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nstcalcenergy = 10
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nstenergy = NENERGY
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nstxout-compressed = NSTXOUT
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compressed-x-precision = 1000
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energygrps = system
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rlist = 1.2
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nstlist = 10
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coulombtype = pme
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rcoulomb = 1.2
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coulomb-modifier = potential-shift-verlet
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vdwtype = pme
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rvdw = 1.2
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vdw-modifier = potential-shift-verlet
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fourierspacing = 0.144
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tcoupl = v-rescale
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tau_t = TAUT
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gen_vel = yes
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gen_temp = TEMP
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ref_t = TEMP
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tc-grps = system
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pcoupl = PCOUPL
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tau_p = TAUP
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ref_p = PRESSURE
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compressibility = 4.5e-5
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nstpcouple = 10
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nsttcouple = 10
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EOF
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#=====================================================================================
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cat > params_emin.ini << EOF
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INTEGRATOR = steep
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NSTEPS = 10000
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NLOG = 100
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NENERGY = 100
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NSTXOUT = 100
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TAUT = 1.0
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TEMP = 300
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PCOUPL = no
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TCOUPL = no
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TAUP = 1.0
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EOF
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cat > params_an1.ini << EOF
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INTEGRATOR = md
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NSTEPS = 2000000
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NLOG = 1000
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NENERGY = 100
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NSTXOUT = 1000
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TCOUPL = v-rescale
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TAUT = 0.5
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TEMP = 10.0
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PCOUPL = c-rescale
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TAUP = 1.0
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EOF
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#=====================================================================================
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cat > topology.top << EOF
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[ defaults ]
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 2 yes 1.0 1.0
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[atomtypes]
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;name mass charge ptype sigma epsilon
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A MASS 0.000 A SIGMA_A EPSILON_A
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B MASS 0.000 A SIGMA_B EPSILON_B
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D 0 0.000 D 0.0 0.0
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[moleculetype]
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; name nrexcl
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L 1
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[atoms]
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; nr type resnr residu atom cgnr charge
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1 A 1 L A 1 0 MASS
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2 B 1 L B1 1 CHARGE_B MASS
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3 B 1 L B2 1 CHARGE_B MASS
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4 D 1 L D 1 CHARGE_A 0.0
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[settles]
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;i funct doh dhh
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1 1 D_AB D_BB
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[dummies3]
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; Dummy from funct a b
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4 1 2 3 1 DUMMY_AB DUMMY_AB
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[exclusions]
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1 2 3 4
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2 1 3 4
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3 1 2 4
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4 1 2 3
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[system]
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MODEL
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[molecules]
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L NMOL
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EOF
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#=====================================================================================
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bash ../create_emin.sh
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bash ../create_annealing1.sh
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#=====================================================================================
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echo "finished and simulation directory $DIRECTORY created and filled"
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ls
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exit 0
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