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2d_umbrella_sampling_executable

#!/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 · Last modified: 2016/03/07 14:25 by root