Subashini .K subashinik at hotmail.com
Tue Feb 28 08:14:23 CET 2017

Hi gromacs users,

I use the following run.sh in the working directory of simulations

set -e

for ((i=0;i<27;i++)); do

    x=$(echo "0.05*$(($i+1))" | bc);

    sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
    gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
    gmx mdrun -deffnm min.$i -pf pullf-min.$i -px pullx-min.$i

    sed 's/WINDOW/'$x'/g' mdp/min2.mdp > grompp.mdp
    gmx grompp -o min2.$i -c min.$i -t min.$i -pp min2.$i -po min2.$i -maxwarn 1 -n index.ndx
    gmx mdrun -deffnm min2.$i -pf pullf-min2.$i -px pullx-min2.$i

    sed 's/WINDOW/'$x'/g' mdp/eql.mdp > grompp.mdp
    gmx grompp -o eql.$i -c min2.$i -t min2.$i -pp eql.$i -po eql.$i -n index.ndx
    gmx mdrun -deffnm eql.$i -pf pullf-eql.$i -px pullx-eql.$i

    sed 's/WINDOW/'$x'/g' mdp/eql2.mdp > grompp.mdp
    gmx grompp -o eql2.$i -c eql.$i -t eql.$i -pp eql2.$i -po eql2.$i -n index.ndx
    gmx mdrun -deffnm eql2.$i -pf pullf-eql2.$i -px pullx-eql2.$i

    sed 's/WINDOW/'$x'/g' mdp/prd.mdp > grompp.mdp
    gmx grompp -o prd.$i -c eql2.$i -t eql2.$i -pp prd.$i -po prd.$i -n index.ndx
    gmx mdrun -deffnm prd.$i -pf pullf-prd.$i -px pullx-prd.$i


However, I get the following error

: invalid option: set: -
set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
./run.sh: line 3: $'\r': command not found
./run.sh: line 4: syntax error near unexpected token `$'do\r''
'/run.sh: line 4: `for ((i=0;i<27;i++)); do

How to fix it?



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