creat_mdp_replic.sh

#!/bin/bash


for counter in {1..54}; do

	val=$((counter-1))
	name=nvt_eq${val}
	file=${name}${val}.mdp

	echo $val
	mkdir $name
	cp npt.mdp ./${name}/${file}

	echo "; Free energy control stuff" >> ./${name}/${file}
	echo "free_energy		= yes" >> ./${name}/${file}
	echo "init_lambda_state		= $val" >> ./${name}/${file}
	echo "delta_lambda		= 0" >> ./${name}/${file}
	echo "fep-lambdas		= 0, 0.02953465509, 0.05841603299, 0.08676540472, 0.1144859813, 0.1416919401, 0.1683888655, 0.1945366201, 0.2202351467, 0.2453571019, 0.2698759515, 0.294093178, 0.3178042393, 0.3410579142, 0.3638979829, 0.3863282163, 0.4082841371, 0.4298098926, 0.4509773599, 0.4717569147, 0.492093157, 0.5121136026, 0.5317612252, 0.5510413812, 0.5699860646, 0.5884184791, 0.606682419, 0.6245980707, 0.6422180959, 0.6595214357, 0.6764023231, 0.6931090711, 0.7095100779, 0.7256297438, 0.7414707238, 0.7570358602, 0.7723281625, 0.7873684404, 0.8025517938, 0.8170647191, 0.8313326801, 0.8453578936, 0.8591276238, 0.8726897497, 0.8860157986, 0.89910859, 0.9119844209, 0.9246450974, 0.9371051654, 0.9493533825, 0.9613920058, 0.9732348938, 0.9848834837, 0.9963393626, 1" >> ./${name}/${file}
	echo "couple-intramol		= yes" >> ./${name}/${file}
	echo "" >> ./${name}/${file}
done