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2d_umbrella_sampling_executable [2016/03/07 14:25] (current)
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 +''#​!/​bin/​bash''​\\
 +\\
 +#Defing here the environment variables (mpd,​AMBERHOME,​...)\\
 +\\
 +#1.- LIMITS FOR x AND y VARIABLES\\
 +''​xstart=4.00''​\\
 +''​xend=1.00''​\\
 +''​xdecrement=-0.50''​\\
 +''​xincrement=0.50''​\\
 +\\
 +''​ystart=1.90''​\\
 +''​yend=1.00''​\\
 +''​ydecrement=-0.15''​\\
 +''​yincrement=0.15''​\\
 +\\
 +#2.- MD CONDITIONS DEFINITIONS\\
 +\\
 +''​nstlimp=20000''​\\
 +''​nstlime=100''​\\
 +''​idmumbt=10''​\\
 +''​ku=1000.0''​\\
 +\\
 +''​for x in `seq -f %1.2f $xstart $xdecrement $xend`; do''​\\
 +''​for y in `seq -f %1.2f $ystart $ydecrement $yend`; do''​\\
 +\\
 +''​touch empty.txt''​\\
 +\\
 +''​xincre=`awk '​BEGIN{printf"​%1.2f",'​$x'​+'​$xdecrement'​}'​ empty.txt`''​\\
 +''​yincre=`awk '​BEGIN{printf"​%1.2f",'​$y'​+'​$ydecrement'​}'​ empty.txt`''​\\
 +\\
 +#3.- EQUILIBRATION INPUT\\
 +\\
 +''​cat > ./​eq.$x.$y.in <<​eof''​\\
 +''​umbrella sampling''​\\
 +''&​cntrl''​\\
 + ''​ntx = 1, irest = 0, ntrx = 1,''​\\
 + ''​ntxo = 1,''​\\
 + ''​ntpr = 100, ntwx =100,''​\\
 + ''​ntf = 1, ntb = 2, dielc = 1.0,''​\\
 +''​cut = 10., nsnb = 10,''​\\
 + ''​imin = 0, ibelly = 0,''​\\
 +''​nstlim = $nstlime, dt = 0.0005,''​\\
 +''​temp0 = 300.0, tempi = 300.0,''​\\
 + ''​ntt = 1, vlimit = 20.0,''​\\
 + ''​ntp = 1,''​\\
 + ''​ntc = 1, tol = 0.00001, pres0=1, comp=44.6,''​\\
 + ''​jfastw=0,​ nscm=1000,''​\\
 + ''​ifqnt=1,​ nmropt=1,''​\\
 +''&​end''​\\
 +''&​qmmm''​\\
 +''​iqmatoms=626,​627,​628,​629,​630,​631,​632,​633,​634,​635,''​\\
 +''​5021,​5022,​5023,​5024,​5025,​5026,​5027,​5028,​5029,​5030,​5031,​5032,​5033,''​\\
 +''​5034,​5035,​5036,​5037,​5038,​5039,​5040,​5041,​5042,​5043,​5044,​5045,​5046,​5047,​5048,​5049,​5050,​5051,​5052,​5053,​5054,​5055,​5056,​5057,​5058,​5059,​5060,​5061,​5062,''​\\
 +''​601,​602,​603,​604,''​\\
 +''​673,​674,​675,​676,​677,​678,​679,​680,​681,​682,​683,​684,''​\\
 +''​883,​884,​885,​886,​887,​888,​889,​890,​891,​892,''​\\
 +''​2121,​2122,​2123,​2124,''​\\
 +''​5020,''​\\
 +''​qmcharge=0,''​\\
 +''​qm_theory='​DFTB',''​\\
 +''​qmshake=0,''​\\
 +''​writepdb=1,''​\\
 +''​verbosity=0,''​\\
 +''​diag_routine=0,''​\\
 +''​dftb_telec=100,''​\\
 +''&​end''​\\
 +''&​wt''​\\
 +''​type='​DUMPFREQ',​ istep1=5,''​\\
 +''&​end''​\\
 +''&​wt''​\\
 +''​type="​END",''​\\
 +''&​end''​\\
 +''​DISANG=./​va.$x.$y.RST''​\\
 +''​DUMPAVE=./​va.$x.$y.eq''​\\
 +\\
 +#4.- RESTRAINT FILE\\
 +\\
 +''​cat > ./​va.$x.$y.RST <<​eof''​\\
 +''&​rst''​\\
 +''​iat=5043,​5022,​ r1=-20, r2=$x, r3=$x, r4=20, rk2=$ku, rk3=$ku,''​\\
 +''&​end''​\\
 +''&​rst''​\\
 +''​iat=635,​5021,​ r1=-20, r2=$y, r3=$y, r4=20, rk2=$ku, rk3=$ku,''​\\
 +''&​end''​\\
 +''​eof''​\\
 +\\
 +''​done''​\\
 +''​done''​\\
 +\\
 +''​xT=${xstart}''​\\
 +''​for x in `seq -f %1.2f $xstart $xdecrement $xend`; do''​\\
 +''​yT=${ystart}''​\\
 +''​for y in `seq -f %1.2f $ystart $ydecrement $yend`; do''​\\
 +\\
 +''​if ! [ ${x} == 4.00 -a ${y} == 1.90 ]''​\\
 +''​then''​\\
 +        ''​chmod 755 eq.$x.$y.in''​\\
 +        ''​$DO_PARALLEL $AMBERHOME/​bin/​sander.MPI -O -i ./​eq.$x.$y.in -o ./​eq.$x.$y.out -p ./​dimerIBAbis.top -c ./​eq.${xT}.${yT}.rst -r ./​eq.$x.$y.rst -inf ./mdinfo -x ./​eq.$x.$y.trj''​\\
 +        ''#​echo ./​eq.$x.$y.in -o ./​eq.$x.$y.out -p ./​dimerIBAbis.top -c ./​eq.${xT}.${yT}.rst -r ./​eq.$x.$y.rst -inf ./mdinfo -x ./​eq.$x.$y.trj''​\\
 +\\
 +''​xT=$x''​\\
 +''​yT=$y''​\\
 +''​done''​\\
 +''​done''​\\
 +\\
 +''​eof''​\\
 +\\
  
2d_umbrella_sampling_executable.txt ยท Last modified: 2016/03/07 14:25 by root