fix swap good

main.c

@@ -199,7 +199,7 @@ void simulate(Chain * chain, Chaint *chaint, Biasmap* biasmap, simulation_params
 		int stopSignal = 0;
 		int swapInd = 0;
 		int swapInd2 = 0;
-		int swapLength = 20; //size of swapping pool
+		int swapLength = 10; //size of swapping pool
 		int inCache = 0;
 		int ind = 0;
 		int currIndex = 0;
@@ -215,7 +215,7 @@ void simulate(Chain * chain, Chaint *chaint, Biasmap* biasmap, simulation_params
 		int noImprovStopSteps = 20000000;
 		int swapBadSteps = 200000;
 		int swapGoodSteps = 200000;
-		double goodEnergyDiff = 8.33; //5kcal
+		double goodEnergyDiff = 5; //5kcal=8.33
 		double rmsdCutoff = 2.0; // swapping clusters rmsd cutoff
 		double heatFactor = 0.5; // starting temp while annealing
 		double annealFactor = 1.02; // 1.02^35 = 1.015^47 = 1.012^58 = 2 ,first 35 *10000 to reach room temperature

metropolis.c

@@ -90,7 +90,7 @@ static int allowed(Chain *chain, Chaint *chaint, Biasmap* biasmap, int start, in
 	double internalloss = loss;
 	double external_k = 1.0;
 	if (sim_params->protein_model.external_potential_type == 5 || sim_params->protein_model.external_potential_type2 == 4)	external_k = sim_params->protein_model.external_k[0];
-	if (q > 0) external_k = 0.02 * external_k;
+	if (q > 0 || externalloss < -10 ) external_k = 0.1 * external_k;
 	//loss is negative!! if loss is negative, it's worse, bad
 	/* Metropolis criteria */
 	//loss += q - chain->Erg(0, 0);
@@ -113,14 +113,14 @@ static int allowed(Chain *chain, Chaint *chaint, Biasmap* biasmap, int start, in
 
 
 
-	if (loss < 0.0  && !sim_params->NS &&  exp(sim_params->thermobeta * (loss)) * RAND_MAX < external_k * rand()) {
+	if (loss < 0.0  && !sim_params->NS &&  exp(sim_params->thermobeta * loss) * RAND_MAX < external_k * rand()) {
 		//fprintf(stderr," rejected\n");
 		return 0;	/* disregard rejected changes */
 	}
 
-    if (sim_params->protein_model.external_potential_type == 5 && externalloss < 0.0 && !sim_params->NS &&   sim_params->thermobeta * externalloss * RAND_MAX * external_k < - rand()) {
-        return 0;
-    }
+	if (sim_params->protein_model.external_potential_type == 5 && externalloss < 0.0 && !sim_params->NS &&   sim_params->thermobeta * externalloss * RAND_MAX * external_k < -rand()) {
+		return 0;
+	}
 	//
 	//if (sim_params->protein_model.external_potential_type == 5 && q >= 10 && !sim_params->NS && externalloss < 0.0 &&   exp(sim_params->thermobeta * externalloss) * RAND_MAX < external_k * rand()) {
 	//	//fprintf(stderr," rejected\n");

vdw.c

@@ -186,14 +186,14 @@ double clash(AA *a, model_params *mod_params)
 double HHvDW(AA *a, AA *b) 
 {
 	double HHradii = 2.6;
-	double HHstrength = 0.077;
+	double HHstrength = 0.1;
 	if (a->id == 'P' || b->id == 'P') return 0.;
 	double distHH = distance(a->h, b->h);
 	if (distHH >= 9) return 0.;
 	double p6 = (HHradii*HHradii/distHH) * (HHradii*HHradii/distHH) *(HHradii*HHradii/distHH);
         double erg=0.;
 	if (a->id != 'P' && b->id != 'P' && distHH<9) {
-		erg = 1/sqrt(distHH) + HHstrength * (p6*p6-2*p6) - 0.282;
+		erg = 1/sqrt(distHH) + HHstrength * (p6*p6-2*p6) - 0.2665;
 		//fprintf(stderr, "close exN HH %g\n", erg);
 	}
         return erg;