#!/bin/csh -f #*********************************** # Orlando Acevedo AMBER 14 job template #*********************************** #BSUB -n 1 #BSUB -q gpu #BSUB -W 168:00 #BSUB -J aMD_WT #BSUB -P prmt #BSUB -o %J.out #BSUB -e %J.err #BSUB -x # Choose which MD protocol to use # (1) pmemd.cuda is for single GPU # (2) pmemd.cuda.MPI is for multiprocessor GPU # (3) pmemd is for single CPU # (4) pmemd.MPI is for multiprocessor CPU # (5) sander is for single CPU # (6) sander.MPI is for multiprocessor CPU # $AMBERHOME/bin/pmemd.cuda # $AMBERHOME/bin/pmemd.cuda.MPI # $AMBERHOME/bin/pmemd # $AMBERHOME/bin/pmemd.MPI # $AMBERHOME/bin/sander # $AMBERHOME/bin/sander.MPI # Set job name and current dir set user = axt651 set jobname = PRMT1-WT_aMD set local = /projects/chem/ionic/abhi/PRMT-1_dimer/WT/HMR/igb_5/aMD_3 set amber=$AMBERHOME/bin/pmemd.cuda # Copy AMBER files to scratch dir #mkdir /scratch/projects/prmt/$user mkdir /scratch/projects/prmt/$user/$jobname cd /scratch/projects/prmt/$user/$jobname # Usually need a parameter and restart file cp $local/PRMT1_HR.prmtop parm #cp $local/PRMT1_dimer_avg_10ns.rst restrt #cp $local/PRMT1_dimer_avg_190ns.rst 190restrt #cp $local/PRMT1_dimer_avg_300ns.rst 300restrt #cp $local/PRMT1_dimer_avg_520ns.rst 520restrt cp $local/PRMT1_dimer_avg_740ns.rst 740restrt # Write input below cat > mdin << EOF &cntrl imin=0,irest=1,ntx=5, nstlim=2500000,dt=0.004, ntf=2,ntc=2,ntb=0,ig=-1, igb=5,cut=999.0,rgbmax=15.0, ntpr=500, ntwx=500, ntwr=10000, saltcon=0.2, gamma_ln=50, tempi=300, temp0=300.0, ntt=3,tautp=1.0, nscm=100, iamd=3, ethreshp=-11282,alphap=2142, ethreshd=10681,alphad=461, / &ewald dsum_tol=0.000001, / &end EOF #gamma_ln, The collision frequency γ, in ps−1, when ntt = 3. Default is 0. #No periodocity constant temperature averaging 10ns #&cntrl # imin = 0, ntb = 0, ntp = 0, ntc = 2, ntf = 2, tol = 0.000001, # igb = 8, gbsa = 1, ntpr = 500, ntwx = 500, ntwr = 10000, # ntt = 3, gamma_ln = 91.0, saltcon = 0.2, # temp0 = 300.0, intdiel = 1.0, # nstlim = 10000000, dt = 0.001, nrespa = 1, # rgbmax = 16.0, ioutfm = 1, cut=9999., #&end #EOF export CUDA_VISIBLE_DEVICES=0 #$amber -O -i mdin -p parm -c restrt -r PRMT1_dimer_avg_10ns.rst -x PRMT1_dimer_avg_10ns.crd -o PRMT1_dimer_avg_10ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_10ns.rst -r PRMT1_dimer_avg_20ns.rst -x PRMT1_dimer_avg_20ns.crd -o PRMT1_dimer_avg_20ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_20ns.rst -r PRMT1_dimer_avg_30ns.rst -x PRMT1_dimer_avg_30ns.crd -o PRMT1_dimer_avg_30ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_30ns.rst -r PRMT1_dimer_avg_40ns.rst -x PRMT1_dimer_avg_40ns.crd -o PRMT1_dimer_avg_40ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_40ns.rst -r PRMT1_dimer_avg_50ns.rst -x PRMT1_dimer_avg_50ns.crd -o PRMT1_dimer_avg_50ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_50ns.rst -r PRMT1_dimer_avg_60ns.rst -x PRMT1_dimer_avg_60ns.crd -o PRMT1_dimer_avg_60ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_60ns.rst -r PRMT1_dimer_avg_70ns.rst -x PRMT1_dimer_avg_70ns.crd -o PRMT1_dimer_avg_70ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_70ns.rst -r PRMT1_dimer_avg_80ns.rst -x PRMT1_dimer_avg_80ns.crd -o PRMT1_dimer_avg_80ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_80ns.rst -r PRMT1_dimer_avg_90ns.rst -x PRMT1_dimer_avg_90ns.crd -o PRMT1_dimer_avg_90ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_90ns.rst -r PRMT1_dimer_avg_100ns.rst -x PRMT1_dimer_avg_100ns.crd -o PRMT1_dimer_avg_100ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_100ns.rst -r PRMT1_dimer_avg_110ns.rst -x PRMT1_dimer_avg_110ns.crd -o PRMT1_dimer_avg_110ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_110ns.rst -r PRMT1_dimer_avg_120ns.rst -x PRMT1_dimer_avg_120ns.crd -o PRMT1_dimer_avg_120ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_120ns.rst -r PRMT1_dimer_avg_130ns.rst -x PRMT1_dimer_avg_130ns.crd -o PRMT1_dimer_avg_130ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_130ns.rst -r PRMT1_dimer_avg_140ns.rst -x PRMT1_dimer_avg_140ns.crd -o PRMT1_dimer_avg_140ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_140ns.rst -r PRMT1_dimer_avg_150ns.rst -x PRMT1_dimer_avg_150ns.crd -o PRMT1_dimer_avg_150ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_150ns.rst -r PRMT1_dimer_avg_160ns.rst -x PRMT1_dimer_avg_160ns.crd -o PRMT1_dimer_avg_160ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_160ns.rst -r PRMT1_dimer_avg_170ns.rst -x PRMT1_dimer_avg_170ns.crd -o PRMT1_dimer_avg_170ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_170ns.rst -r PRMT1_dimer_avg_180ns.rst -x PRMT1_dimer_avg_180ns.crd -o PRMT1_dimer_avg_180ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_180ns.rst -r PRMT1_dimer_avg_190ns.rst -x PRMT1_dimer_avg_190ns.crd -o PRMT1_dimer_avg_190ns.out #$amber -O -i mdin -p parm -c 190restrt -r PRMT1_dimer_avg_200ns.rst -x PRMT1_dimer_avg_200ns.crd -o PRMT1_dimer_avg_200ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_200ns.rst -r PRMT1_dimer_avg_210ns.rst -x PRMT1_dimer_avg_210ns.crd -o PRMT1_dimer_avg_210ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_210ns.rst -r PRMT1_dimer_avg_220ns.rst -x PRMT1_dimer_avg_220ns.crd -o PRMT1_dimer_avg_220ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_220ns.rst -r PRMT1_dimer_avg_230ns.rst -x PRMT1_dimer_avg_230ns.crd -o PRMT1_dimer_avg_230ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_230ns.rst -r PRMT1_dimer_avg_240ns.rst -x PRMT1_dimer_avg_240ns.crd -o PRMT1_dimer_avg_240ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_240ns.rst -r PRMT1_dimer_avg_250ns.rst -x PRMT1_dimer_avg_250ns.crd -o PRMT1_dimer_avg_250ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_250ns.rst -r PRMT1_dimer_avg_260ns.rst -x PRMT1_dimer_avg_260ns.crd -o PRMT1_dimer_avg_260ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_260ns.rst -r PRMT1_dimer_avg_270ns.rst -x PRMT1_dimer_avg_270ns.crd -o PRMT1_dimer_avg_270ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_270ns.rst -r PRMT1_dimer_avg_280ns.rst -x PRMT1_dimer_avg_280ns.crd -o PRMT1_dimer_avg_280ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_280ns.rst -r PRMT1_dimer_avg_290ns.rst -x PRMT1_dimer_avg_290ns.crd -o PRMT1_dimer_avg_290ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_290ns.rst -r PRMT1_dimer_avg_300ns.rst -x PRMT1_dimer_avg_300ns.crd -o PRMT1_dimer_avg_300ns.out #$amber -O -i mdin -p parm -c 300restrt -r PRMT1_dimer_avg_310ns.rst -x PRMT1_dimer_avg_310ns.crd -o PRMT1_dimer_avg_310ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_310ns.rst -r PRMT1_dimer_avg_320ns.rst -x PRMT1_dimer_avg_320ns.crd -o PRMT1_dimer_avg_320ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_320ns.rst -r PRMT1_dimer_avg_330ns.rst -x PRMT1_dimer_avg_330ns.crd -o PRMT1_dimer_avg_330ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_330ns.rst -r PRMT1_dimer_avg_340ns.rst -x PRMT1_dimer_avg_340ns.crd -o PRMT1_dimer_avg_340ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_340ns.rst -r PRMT1_dimer_avg_350ns.rst -x PRMT1_dimer_avg_350ns.crd -o PRMT1_dimer_avg_350ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_350ns.rst -r PRMT1_dimer_avg_360ns.rst -x PRMT1_dimer_avg_360ns.crd -o PRMT1_dimer_avg_360ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_360ns.rst -r PRMT1_dimer_avg_370ns.rst -x PRMT1_dimer_avg_370ns.crd -o PRMT1_dimer_avg_370ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_370ns.rst -r PRMT1_dimer_avg_380ns.rst -x PRMT1_dimer_avg_380ns.crd -o PRMT1_dimer_avg_380ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_380ns.rst -r PRMT1_dimer_avg_390ns.rst -x PRMT1_dimer_avg_390ns.crd -o PRMT1_dimer_avg_390ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_390ns.rst -r PRMT1_dimer_avg_400ns.rst -x PRMT1_dimer_avg_400ns.crd -o PRMT1_dimer_avg_400ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_400ns.rst -r PRMT1_dimer_avg_410ns.rst -x PRMT1_dimer_avg_410ns.crd -o PRMT1_dimer_avg_410ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_410ns.rst -r PRMT1_dimer_avg_420ns.rst -x PRMT1_dimer_avg_420ns.crd -o PRMT1_dimer_avg_420ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_420ns.rst -r PRMT1_dimer_avg_430ns.rst -x PRMT1_dimer_avg_430ns.crd -o PRMT1_dimer_avg_430ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_430ns.rst -r PRMT1_dimer_avg_440ns.rst -x PRMT1_dimer_avg_440ns.crd -o PRMT1_dimer_avg_440ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_440ns.rst -r PRMT1_dimer_avg_450ns.rst -x PRMT1_dimer_avg_450ns.crd -o PRMT1_dimer_avg_450ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_450ns.rst -r PRMT1_dimer_avg_460ns.rst -x PRMT1_dimer_avg_460ns.crd -o PRMT1_dimer_avg_460ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_460ns.rst -r PRMT1_dimer_avg_470ns.rst -x PRMT1_dimer_avg_470ns.crd -o PRMT1_dimer_avg_470ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_470ns.rst -r PRMT1_dimer_avg_480ns.rst -x PRMT1_dimer_avg_480ns.crd -o PRMT1_dimer_avg_480ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_480ns.rst -r PRMT1_dimer_avg_490ns.rst -x PRMT1_dimer_avg_490ns.crd -o PRMT1_dimer_avg_490ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_490ns.rst -r PRMT1_dimer_avg_500ns.rst -x PRMT1_dimer_avg_500ns.crd -o PRMT1_dimer_avg_500ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_500ns.rst -r PRMT1_dimer_avg_510ns.rst -x PRMT1_dimer_avg_510ns.crd -o PRMT1_dimer_avg_510ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_510ns.rst -r PRMT1_dimer_avg_520ns.rst -x PRMT1_dimer_avg_520ns.crd -o PRMT1_dimer_avg_520ns.out #$amber -O -i mdin -p parm -c 520restrt -r PRMT1_dimer_avg_530ns.rst -x PRMT1_dimer_avg_530ns.crd -o PRMT1_dimer_avg_530ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_530ns.rst -r PRMT1_dimer_avg_540ns.rst -x PRMT1_dimer_avg_540ns.crd -o PRMT1_dimer_avg_540ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_540ns.rst -r PRMT1_dimer_avg_550ns.rst -x PRMT1_dimer_avg_550ns.crd -o PRMT1_dimer_avg_550ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_550ns.rst -r PRMT1_dimer_avg_560ns.rst -x PRMT1_dimer_avg_560ns.crd -o PRMT1_dimer_avg_560ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_560ns.rst -r PRMT1_dimer_avg_570ns.rst -x PRMT1_dimer_avg_570ns.crd -o PRMT1_dimer_avg_570ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_570ns.rst -r PRMT1_dimer_avg_580ns.rst -x PRMT1_dimer_avg_580ns.crd -o PRMT1_dimer_avg_580ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_580ns.rst -r PRMT1_dimer_avg_590ns.rst -x PRMT1_dimer_avg_590ns.crd -o PRMT1_dimer_avg_590ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_590ns.rst -r PRMT1_dimer_avg_600ns.rst -x PRMT1_dimer_avg_600ns.crd -o PRMT1_dimer_avg_600ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_600ns.rst -r PRMT1_dimer_avg_610ns.rst -x PRMT1_dimer_avg_610ns.crd -o PRMT1_dimer_avg_610ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_610ns.rst -r PRMT1_dimer_avg_620ns.rst -x PRMT1_dimer_avg_620ns.crd -o PRMT1_dimer_avg_620ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_620ns.rst -r PRMT1_dimer_avg_630ns.rst -x PRMT1_dimer_avg_630ns.crd -o PRMT1_dimer_avg_630ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_630ns.rst -r PRMT1_dimer_avg_640ns.rst -x PRMT1_dimer_avg_640ns.crd -o PRMT1_dimer_avg_640ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_640ns.rst -r PRMT1_dimer_avg_650ns.rst -x PRMT1_dimer_avg_650ns.crd -o PRMT1_dimer_avg_650ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_650ns.rst -r PRMT1_dimer_avg_660ns.rst -x PRMT1_dimer_avg_660ns.crd -o PRMT1_dimer_avg_660ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_660ns.rst -r PRMT1_dimer_avg_670ns.rst -x PRMT1_dimer_avg_670ns.crd -o PRMT1_dimer_avg_670ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_670ns.rst -r PRMT1_dimer_avg_680ns.rst -x PRMT1_dimer_avg_680ns.crd -o PRMT1_dimer_avg_680ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_680ns.rst -r PRMT1_dimer_avg_690ns.rst -x PRMT1_dimer_avg_690ns.crd -o PRMT1_dimer_avg_690ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_690ns.rst -r PRMT1_dimer_avg_700ns.rst -x PRMT1_dimer_avg_700ns.crd -o PRMT1_dimer_avg_700ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_700ns.rst -r PRMT1_dimer_avg_710ns.rst -x PRMT1_dimer_avg_710ns.crd -o PRMT1_dimer_avg_710ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_710ns.rst -r PRMT1_dimer_avg_720ns.rst -x PRMT1_dimer_avg_720ns.crd -o PRMT1_dimer_avg_720ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_720ns.rst -r PRMT1_dimer_avg_730ns.rst -x PRMT1_dimer_avg_730ns.crd -o PRMT1_dimer_avg_730ns.out #$amber -O -i mdin -p parm -c PRMT1_dimer_avg_730ns.rst -r PRMT1_dimer_avg_740ns.rst -x PRMT1_dimer_avg_740ns.crd -o PRMT1_dimer_avg_740ns.out $amber -O -i mdin -p parm -c 740restrt -r PRMT1_dimer_avg_750ns.rst -x PRMT1_dimer_avg_750ns.crd -o PRMT1_dimer_avg_750ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_750ns.rst -r PRMT1_dimer_avg_760ns.rst -x PRMT1_dimer_avg_760ns.crd -o PRMT1_dimer_avg_760ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_760ns.rst -r PRMT1_dimer_avg_770ns.rst -x PRMT1_dimer_avg_770ns.crd -o PRMT1_dimer_avg_770ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_770ns.rst -r PRMT1_dimer_avg_780ns.rst -x PRMT1_dimer_avg_780ns.crd -o PRMT1_dimer_avg_780ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_780ns.rst -r PRMT1_dimer_avg_790ns.rst -x PRMT1_dimer_avg_790ns.crd -o PRMT1_dimer_avg_790ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_790ns.rst -r PRMT1_dimer_avg_800ns.rst -x PRMT1_dimer_avg_800ns.crd -o PRMT1_dimer_avg_800ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_800ns.rst -r PRMT1_dimer_avg_810ns.rst -x PRMT1_dimer_avg_810ns.crd -o PRMT1_dimer_avg_810ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_810ns.rst -r PRMT1_dimer_avg_820ns.rst -x PRMT1_dimer_avg_820ns.crd -o PRMT1_dimer_avg_820ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_820ns.rst -r PRMT1_dimer_avg_830ns.rst -x PRMT1_dimer_avg_830ns.crd -o PRMT1_dimer_avg_830ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_830ns.rst -r PRMT1_dimer_avg_840ns.rst -x PRMT1_dimer_avg_840ns.crd -o PRMT1_dimer_avg_840ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_840ns.rst -r PRMT1_dimer_avg_850ns.rst -x PRMT1_dimer_avg_850ns.crd -o PRMT1_dimer_avg_850ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_850ns.rst -r PRMT1_dimer_avg_860ns.rst -x PRMT1_dimer_avg_860ns.crd -o PRMT1_dimer_avg_860ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_860ns.rst -r PRMT1_dimer_avg_870ns.rst -x PRMT1_dimer_avg_870ns.crd -o PRMT1_dimer_avg_870ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_870ns.rst -r PRMT1_dimer_avg_880ns.rst -x PRMT1_dimer_avg_880ns.crd -o PRMT1_dimer_avg_880ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_880ns.rst -r PRMT1_dimer_avg_890ns.rst -x PRMT1_dimer_avg_890ns.crd -o PRMT1_dimer_avg_890ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_890ns.rst -r PRMT1_dimer_avg_900ns.rst -x PRMT1_dimer_avg_900ns.crd -o PRMT1_dimer_avg_900ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_900ns.rst -r PRMT1_dimer_avg_910ns.rst -x PRMT1_dimer_avg_910ns.crd -o PRMT1_dimer_avg_910ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_910ns.rst -r PRMT1_dimer_avg_920ns.rst -x PRMT1_dimer_avg_920ns.crd -o PRMT1_dimer_avg_920ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_920ns.rst -r PRMT1_dimer_avg_930ns.rst -x PRMT1_dimer_avg_930ns.crd -o PRMT1_dimer_avg_930ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_930ns.rst -r PRMT1_dimer_avg_940ns.rst -x PRMT1_dimer_avg_940ns.crd -o PRMT1_dimer_avg_940ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_940ns.rst -r PRMT1_dimer_avg_950ns.rst -x PRMT1_dimer_avg_950ns.crd -o PRMT1_dimer_avg_950ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_950ns.rst -r PRMT1_dimer_avg_960ns.rst -x PRMT1_dimer_avg_960ns.crd -o PRMT1_dimer_avg_960ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_960ns.rst -r PRMT1_dimer_avg_970ns.rst -x PRMT1_dimer_avg_970ns.crd -o PRMT1_dimer_avg_970ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_970ns.rst -r PRMT1_dimer_avg_980ns.rst -x PRMT1_dimer_avg_980ns.crd -o PRMT1_dimer_avg_980ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_980ns.rst -r PRMT1_dimer_avg_990ns.rst -x PRMT1_dimer_avg_990ns.crd -o PRMT1_dimer_avg_990ns.out $amber -O -i mdin -p parm -c PRMT1_dimer_avg_990ns.rst -r PRMT1_dimer_avg_100ns.rst -x PRMT1_dimer_avg_100ns.crd -o PRMT1_dimer_avg_100ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_210ns.rst -r PRMT7_WT_NH1_aMD_avg_220ns.rst -x PRMT7_WT_NH1_aMD_avg_220ns.crd -o PRMT7_WT_NH1_aMD_avg_220ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_220ns.rst -r PRMT7_WT_NH1_aMD_avg_230ns.rst -x PRMT7_WT_NH1_aMD_avg_230ns.crd -o PRMT7_WT_NH1_aMD_avg_230ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_230ns.rst -r PRMT7_WT_NH1_aMD_avg_240ns.rst -x PRMT7_WT_NH1_aMD_avg_240ns.crd -o PRMT7_WT_NH1_aMD_avg_240ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_240ns.rst -r PRMT7_WT_NH1_aMD_avg_250ns.rst -x PRMT7_WT_NH1_aMD_avg_250ns.crd -o PRMT7_WT_NH1_aMD_avg_250ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_250ns.rst -r PRMT7_WT_NH1_aMD_avg_260ns.rst -x PRMT7_WT_NH1_aMD_avg_260ns.crd -o PRMT7_WT_NH1_aMD_avg_260ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_260ns.rst -r PRMT7_WT_NH1_aMD_avg_270ns.rst -x PRMT7_WT_NH1_aMD_avg_270ns.crd -o PRMT7_WT_NH1_aMD_avg_270ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_270ns.rst -r PRMT7_WT_NH1_aMD_avg_280ns.rst -x PRMT7_WT_NH1_aMD_avg_280ns.crd -o PRMT7_WT_NH1_aMD_avg_280ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_280ns.rst -r PRMT7_WT_NH1_aMD_avg_290ns.rst -x PRMT7_WT_NH1_aMD_avg_290ns.crd -o PRMT7_WT_NH1_aMD_avg_290ns.out #$AMBERHOME/bin/pmemd.cuda -O -i mdin -p parm -c PRMT7_WT_NH1_aMD_avg_290ns.rst -r PRMT7_WT_NH1_aMD_avg_300ns.rst -x PRMT7_WT_NH1_aMD_avg_300ns.crd -o PRMT7_WT_NH1_aMD_avg_300ns.out # Delete files rm mdinfo mdin parm restrt # Compress files gzip *.crd *.rst *.out # Copy output files and return to local dir cp * $local/. cd #remove scratch rm -r /scratch/projects/prmt/$user/$jobname