included cutoff=8A only for vdw and hb

Makefile

@@ -202,11 +202,11 @@ odock: check-env-all stringify $(SRC)
 # 3tmn: for testing gradients of torsion genes (1 torsion)
 
 PDB      := 3ce3
-NRUN     := 100
-POPSIZE  := 150
+NRUN     := 200
+POPSIZE  := 500
 TESTNAME := test
-TESTLS   := sd
-NUM_LSIT := 30
+TESTLS   := sw
+NUM_LSIT := 300
 
 test: odock
 	$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 1 -lsmet $(TESTLS) -lsit $(NUM_LSIT) -smooth 0.5

device/calcenergy.cl

@@ -442,11 +442,6 @@ if (get_local_id (0) == 0) {
 		// Calculating atomic_distance
 		float atomic_distance = native_sqrt(subx*subx + suby*suby + subz*subz)*dockpars_grid_spacing;
 
-		// Calculating energy contributions
-/*
-		if (atomic_distance < 8.0f)
-		{
-*/
 		// Getting type IDs
 		uint atom1_typeid = atom_types_const[atom1_id];
 		uint atom2_typeid = atom_types_const[atom2_id];
@@ -463,16 +458,10 @@ if (get_local_id (0) == 0) {
 
 		if (intraE_contributors_const[3*contributor_counter+2] == 1)	//H-bond
 		{
-#if 0
-				opt_distance = reqm_hbond [atom1_typeid] + reqm_hbond [atom2_typeid];
-#endif
 			opt_distance = reqm_hbond [atom1_type_vdw_hb] + reqm_hbond [atom2_type_vdw_hb];
 		}
 		else	//van der Waals
 		{
-#if 0
-				opt_distance = 0.5f*(reqm [atom1_typeid] + reqm [atom2_typeid]);
-#endif
 			opt_distance = 0.5f*(reqm [atom1_type_vdw_hb] + reqm [atom2_type_vdw_hb]);
 		}
 
@@ -491,6 +480,12 @@ if (get_local_id (0) == 0) {
 			smoothed_distance = atomic_distance - delta_distance;
 		}
 
+		// Calculating energy contributions
+		// Cuttoff: internuclear-distance at 8A.
+		// Cutoff only for vdw and hbond.
+		// el and sol contributions are calculated at all distances.
+		if (atomic_distance < 8.0f)
+		{
 			// Calculating van der Waals / hydrogen bond term
 			partial_energies[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));
 #if 0
@@ -521,6 +516,7 @@ raw_intraE_vdw_hb      -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_
 				partial_intraE[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));
 				#endif
 			}
+		} // if cuttoff - internuclear-distance at 8A	
 
 		// Calculating electrostatic term
        		partial_energies[get_local_id(0)] += native_divide (
@@ -613,19 +609,6 @@ raw_intraE_sol = ((dspars_S_const[atom1_typeid] +
 			}
 #endif
 
-
-
-
-
-
-
-
-
-/*
-		} // if (atomic_distance < 8.0f)
-*/
-
-
 	} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)
 
 #if 0

device/calcgradient.cl

@@ -605,9 +605,6 @@ void gpu_calc_gradient(
 		float dist = native_sqrt(subx*subx + suby*suby + subz*subz);
 		float atomic_distance = dist*dockpars_grid_spacing;
 
-		// Calculating gradient contributions
-		if (atomic_distance < 8.0f)
-		{
 		// Getting type IDs
 		uint atom1_typeid = atom_types_const[atom1_id];
 		uint atom2_typeid = atom_types_const[atom2_id];
@@ -625,16 +622,10 @@ void gpu_calc_gradient(
 
 		if (intraE_contributors_const[3*contributor_counter+2] == 1)	//H-bond
 		{
-/*
-				opt_distance = reqm_hbond [atom1_typeid] + reqm_hbond [atom2_typeid];
-*/
 			opt_distance = reqm_hbond [atom1_type_vdw_hb] + reqm_hbond [atom2_type_vdw_hb];
 		}
 		else	//van der Waals
 		{
-/*
-				opt_distance = 0.5f*(reqm [atom1_typeid] + reqm [atom2_typeid]);
-*/
 			opt_distance = 0.5f*(reqm [atom1_type_vdw_hb] + reqm [atom2_type_vdw_hb]);
 		}
 
@@ -653,21 +644,12 @@ void gpu_calc_gradient(
 			smoothed_distance = atomic_distance - delta_distance;
 		}
 
-/*
-			if (get_local_id (0) == 0) {
-
-				if (intraE_contributors_const[3*contributor_counter+2] == 1)	//H-bond
-				{
-					printf("%-5s %u %u %f %f %f %f %f %f\n", "hbond", atom1_typeid, atom2_typeid, reqm_hbond [atom1_typeid], reqm_hbond [atom2_typeid], opt_distance, delta_distance, atomic_distance, smoothed_distance);
-
-				}
-				else	//van der Waals
+		// Calculating gradient contributions
+		// Cuttoff: internuclear-distance at 8A.
+		// Cutoff only for vdw and hbond.
+		// el and sol contributions are calculated at all distances.
+		if (atomic_distance < 8.0f)
 		{
-					printf("%-5s %u %u %f %f %f %f %f %f\n", "vdw", atom1_typeid, atom2_typeid, reqm [atom1_typeid], reqm [atom2_typeid], opt_distance, delta_distance, atomic_distance, smoothed_distance);	
-				}
-			}
-*/
-
 			// Calculating van der Waals / hydrogen bond term
 			priv_gradient_per_intracontributor += native_divide (-12*VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],
 									     native_powr(smoothed_distance/*atomic_distance*/, 13)
@@ -683,6 +665,7 @@ void gpu_calc_gradient(
 										     native_powr(smoothed_distance/*atomic_distance*/, 7)
 										    );
 			}
+		} // if cuttoff - internuclear-distance at 8A	
 
 		// Calculating electrostatic term
 		// http://www.wolframalpha.com/input/?i=1%2F(x*(A%2B(B%2F(1%2BK*exp(-h*B*x)))))
@@ -719,8 +702,6 @@ void gpu_calc_gradient(
 		atomicAdd_g_f(&gradient_intra_x[atom2_id], priv_intra_gradient_x);
 		atomicAdd_g_f(&gradient_intra_y[atom2_id], priv_intra_gradient_y);
 		atomicAdd_g_f(&gradient_intra_z[atom2_id], priv_intra_gradient_z);
-		}
-
 	} // End contributor_counter for-loop (INTRAMOLECULAR ENERGY)