Fix a bug that made VMMC simulate the wrong model when used with the …

…DNA2 interaction

This commit also adds a new test to try to better catch future errors

src/Backends/VMMC_CPUBackend.cpp

@@ -420,17 +420,16 @@ inline number VMMC_CPUBackend::_particle_particle_nonbonded_interaction_VMMC(Bas
 	energy += _interaction->pair_interaction_term(DNAInteraction::NONBONDED_EXCLUDED_VOLUME, p, q, false, false);
 	energy += _interaction->pair_interaction_term(DNAInteraction::CROSS_STACKING, p, q, false, false);
 
-	// all interactions except DNA2Interaction use the DNAInteraction coaxial stacking*
-	// *the hybrid interaction is a second exception
-	if( (dynamic_cast<DNA2Interaction *>(_interaction.get()) == NULL) || (dynamic_cast<DRHInteraction *>(_interaction.get()) == NULL) ) {
+	// the DNA and RNA/RNA2 interactions use the original coaxial stacking term
+	if(dynamic_cast<DNA2Interaction *>(_interaction.get()) == NULL) {
 		energy += _interaction->pair_interaction_term(DNAInteraction::COAXIAL_STACKING, p, q, false, false);
 	}
 
+	// the DNA2 and DRH interactions use DNA2's coaxial stacking term
 	if(dynamic_cast<DRHInteraction *>(_interaction.get()) != NULL) {
 		energy += _interaction->pair_interaction_term(DRHInteraction::COAXIAL_STACKING, p, q, false, false);
 		energy += _interaction->pair_interaction_term(DRHInteraction::DEBYE_HUCKEL, p, q, false, false);
 	}
-
 	else if(dynamic_cast<DNA2Interaction *>(_interaction.get()) != NULL) {
 		energy += _interaction->pair_interaction_term(DNA2Interaction::COAXIAL_STACKING, p, q, false, false);
 		energy += _interaction->pair_interaction_term(DNA2Interaction::DEBYE_HUCKEL, p, q, false, false);

test/DNA/DSDNA8/VMMC/quick_compare

@@ -1 +1 @@
-ColumnAverage::energy.dat::2::-1.37970256144::0.15
+ColumnAverage::energy.dat::2::-1.37970256144::0.01

test/DNA/DSDNA8/VMMC_DNA2/quick_compare

@@ -0,0 +1 @@
+ColumnAverage::energy.dat::2::-1.379235::0.02

test/DNA/DSDNA8/VMMC_DNA2/quick_input

@@ -0,0 +1,38 @@
+####  PROGRAM PARAMETERS  ####
+backend = CPU
+#debug = 1
+#seed = 4982
+
+####    SIM PARAMETERS    ####
+sim_type = VMMC
+ensemble = NVT
+
+interaction_type = DNA2
+salt_concentration = 0.5
+
+delta_translation = 0.22
+delta_rotation = 0.22
+
+steps = 5e5
+newtonian_steps = 103
+diff_coeff = 2.50
+#pt = 0.1
+thermostat = john
+
+T = 20C 
+dt = 0.005
+verlet_skin = 0.5
+
+####    INPUT / OUTPUT    ####
+topology = ../dsdna8.top
+conf_file = ../init.dat
+trajectory_file = trajectory.dat
+refresh_vel = 1
+log_file = log.dat
+no_stdout_energy = 1
+restart_step_counter = 1
+energy_file = energy.dat
+print_conf_interval = 1e5
+print_energy_every = 1e3 
+time_scale = linear
+external_forces = 0

test/DNA/SSDNA15/VMMC/quick_compare

@@ -1 +1 @@
-ColumnAverage::energy.dat::2::-0.700783241758::0.26
+ColumnAverage::energy.dat::2::-0.700783241758::0.15