quick fix to test atomistic systems

setup_sim.sh

@@ -135,9 +135,44 @@ L  1
 L                 NMOL 
 EOF
 
+cat > topology.top << EOF
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               yes              1.0     1.0
+
+[atomtypes]
+;name     mass      charge   ptype    sigma        epsilon
+A     MASS       0.000       A      SIGMA_A         EPSILON_A 
+B     MASS       0.000       A      SIGMA_B         EPSILON_B 
+
+[moleculetype]
+; name nrexcl
+A  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     A   1     L  A   1    CHARGE_A      MASS 
+
+[moleculetype]
+; name nrexcl
+B  1
+
+[atoms]
+; nr type resnr residu atom cgnr charge
+1     B   1     L  B   1    CHARGE_B      MASS 
+
+[system]
+ MODEL 
+
+[molecules]
+A                1000
+B                2000
+EOF
+
 #=====================================================================================
-bash ../create_emin.sh
-bash ../create_annealing1.sh
+echo $(dirname $0)
+bash ".$(dirname $0)/create_emin.sh"
+bash ".$(dirname $0)/create_annealing1.sh"
 
 
 #=====================================================================================