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g_membed.sh

script to reproduce the issue - Daniel Bauer, 12/22/2017 01:22 PM

 
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LOG=embed_2018.log
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GMX=gmx
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echo "grompp" | tee -a $LOG
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$GMX --quiet grompp -f g_membed.mdp -c system.gro -p system.top -o g_membed.tpr --maxwarn 2 2>&1 | tee -a $LOG
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echo "Copy input topology to output topology" | tee -a $LOG
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cp system.top embedded.top
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echo "Run embedding simulation" | tee -a $LOG
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echo Protein Other | $GMX --quiet mdrun -deffnm g_membed -membed embed.dat -mp embedded.top -c embedded.gro 2>&1 | tee -a $LOG