Skip to content

GitLab

Commit dfa9a2c2 authored by lvs's avatar lvs
Browse files

set 20,48f cutoff for elec and desol in host and device in fastergrad

parent 151f046e
Hide whitespace changes
Inline Side-by-side
Makefile
View file @ dfa9a2c2
......@@ -206,11 +206,11 @@ PDB := 3ce3
NRUN := 100
POPSIZE := 150
TESTNAME := test
TESTLS := sd
TESTLS := sw
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 0 -lsmet $(TESTLS) -lsit 30
$(BIN_DIR)/$(TARGET) -ffile ./input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ./input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nrun $(NRUN) -psize $(POPSIZE) -resnam $(TESTNAME) -gfpop 0 -lsmet $(TESTLS)
ASTEX_PDB := 2bsm
ASTEX_NRUN:= 10
......
device/calcenergy.cl
View file @ dfa9a2c2
......@@ -489,99 +489,105 @@ if (get_local_id (0) == 0) {
}
// Calculating energy contributions
// Cuttoff: internuclear-distance at 8A.
// Cutoff only for vdw and hbond.
// el and sol contributions are calculated at all distances.
// Cuttoff1: internuclear-distance at 8A only for vdw and hbond.
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
smoothed_intraE = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,12));
raw_intraE_vdw_hb = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,12));
#endif
#if 0
smoothed_intraE = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,12));
raw_intraE_vdw_hb = native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,12));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += native_divide(VWpars_AC_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,12));
#endif
if (intraE_contributors_const[3*contributor_counter+2] == 1) { //H-bond
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,10));
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,10));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,10));
#endif
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,10));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,10));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
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*/,10));
#endif
}
else { //van der Waals
partial_energies[get_local_id(0)] -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance/*atomic_distance*/,6));
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,6));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,6));
#endif
#if 0
smoothed_intraE -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(smoothed_distance,6));
raw_intraE_vdw_hb -= native_divide(VWpars_BD_const[atom1_typeid * dockpars_num_of_atypes+atom2_typeid],native_powr(atomic_distance ,6));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
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
} // if cuttoff1 - internuclear-distance at 8A
// Calculating electrostatic term
partial_energies[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#if 0
smoothed_intraE += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
raw_intraE_el = native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
// Calculating energy contributions
// Cuttoff2: internuclear-distance at 20.48A only for el and sol.
if (atomic_distance < 20.48f)
{
// Calculating electrostatic term
partial_energies[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#if 0
smoothed_intraE += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
raw_intraE_el = native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += native_divide (
dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id],
atomic_distance * (DIEL_A + native_divide(DIEL_B,(1.0f + DIEL_K*native_exp(-DIEL_B_TIMES_H*atomic_distance))))
);
#endif
// Calculating desolvation term
// 1/25.92 = 0.038580246913580245
partial_energies[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#if 0
smoothed_intraE += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
raw_intraE_sol = ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#endif
// Calculating desolvation term
// 1/25.92 = 0.038580246913580245
partial_energies[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#if 0
smoothed_intraE += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
raw_intraE_sol = ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#endif
#if defined (DEBUG_ENERGY_KERNEL)
partial_intraE[get_local_id(0)] += ((dspars_S_const[atom1_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom1_id]))*dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] +
dockpars_qasp*fabs(atom_charges_const[atom2_id]))*dspars_V_const[atom1_typeid]) *
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#endif
dockpars_coeff_desolv*native_exp(-0.03858025f*native_powr(atomic_distance, 2));
#endif
} // if cuttoff2 - internuclear-distance at 20.48A
......
device/calcgradient.cl
View file @ dfa9a2c2
......@@ -671,9 +671,7 @@ void gpu_calc_gradient(
}
// Calculating gradient contributions
// Cuttoff: internuclear-distance at 8A.
// Cutoff only for vdw and hbond.
// el and sol contributions are calculated at all distances.
// Cuttoff1: internuclear-distance at 8A only for vdw and hbond.
if (atomic_distance < 8.0f)
{
// Calculating van der Waals / hydrogen bond term
......@@ -691,22 +689,27 @@ void gpu_calc_gradient(
native_powr(smoothed_distance/*atomic_distance*/, 7)
);
}
} // if cuttoff - internuclear-distance at 8A
} // if cuttoff1 - 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)))))
float upper = DIEL_A*native_powr(native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K, 2) + (DIEL_B)*native_exp(DIEL_B_TIMES_H*atomic_distance)*(DIEL_B_TIMES_H_TIMES_K*atomic_distance + native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K);
// Calculating energy contributions
// Cuttoff2: internuclear-distance at 20.48A only for el and sol.
if (atomic_distance < 20.48f)
{
// Calculating electrostatic term
// http://www.wolframalpha.com/input/?i=1%2F(x*(A%2B(B%2F(1%2BK*exp(-h*B*x)))))
float upper = DIEL_A*native_powr(native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K, 2) + (DIEL_B)*native_exp(DIEL_B_TIMES_H*atomic_distance)*(DIEL_B_TIMES_H_TIMES_K*atomic_distance + native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K);
float lower = native_powr(atomic_distance, 2) * native_powr(DIEL_A * (native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K) + DIEL_B * native_exp(DIEL_B_TIMES_H*atomic_distance), 2);
float lower = native_powr(atomic_distance, 2) * native_powr(DIEL_A * (native_exp(DIEL_B_TIMES_H*atomic_distance) + DIEL_K) + DIEL_B * native_exp(DIEL_B_TIMES_H*atomic_distance), 2);
priv_gradient_per_intracontributor += -dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id] * native_divide (upper, lower);
priv_gradient_per_intracontributor += -dockpars_coeff_elec * atom_charges_const[atom1_id] * atom_charges_const[atom2_id] * native_divide (upper, lower);
// Calculating desolvation term
priv_gradient_per_intracontributor += (
(dspars_S_const[atom1_typeid] + dockpars_qasp*fabs(atom_charges_const[atom1_id])) * dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] + dockpars_qasp*fabs(atom_charges_const[atom2_id])) * dspars_V_const[atom1_typeid]
) *
dockpars_coeff_desolv * -0.07716049382716049 * atomic_distance * native_exp(-0.038580246913580245*native_powr(atomic_distance, 2));
// Calculating desolvation term
priv_gradient_per_intracontributor += (
(dspars_S_const[atom1_typeid] + dockpars_qasp*fabs(atom_charges_const[atom1_id])) * dspars_V_const[atom2_typeid] +
(dspars_S_const[atom2_typeid] + dockpars_qasp*fabs(atom_charges_const[atom2_id])) * dspars_V_const[atom1_typeid]
) *
dockpars_coeff_desolv * -0.07716049382716049 * atomic_distance * native_exp(-0.038580246913580245*native_powr(atomic_distance, 2));
} // if cuttoff2 - internuclear-distance at 20.48A
// Decomposing "priv_gradient_per_intracontributor"
// into the contribution of each atom of the pair
......
host/src/processligand.cpp
View file @ dfa9a2c2
......@@ -2094,23 +2094,25 @@ float calc_intraE_f(const Liganddata* myligand,
if (debug == 1)
printf("van der Waals interaction = ");
}
vW += vdW1 - vdW2;
}
s1 = (myligand->solpar [type_id1] + qasp_mul_absq [atom_id1]);
s2 = (myligand->solpar [type_id2] + qasp_mul_absq [atom_id2]);
v1 = myligand->volume [type_id1];
v2 = myligand->volume [type_id2];
if (dist < 20.48)
{
s1 = (myligand->solpar [type_id1] + qasp_mul_absq [atom_id1]);
s2 = (myligand->solpar [type_id2] + qasp_mul_absq [atom_id2]);
v1 = myligand->volume [type_id1];
v2 = myligand->volume [type_id2];
if (debug == 1)
printf(" %lf, electrostatic = %lf, desolv = %lf\n", (vdW1 - vdW2), q1q2[atom_id1][atom_id2] * r_epsr_table [distance_id],
(s1*v2 + s2*v1) * desolv_table [distance_id]);
if (debug == 1)
printf(" %lf, electrostatic = %lf, desolv = %lf\n", (vdW1 - vdW2), q1q2[atom_id1][atom_id2] * r_epsr_table [distance_id],
(s1*v2 + s2*v1) * desolv_table [distance_id]);
vW += vdW1 - vdW2;
el += q1q2[atom_id1][atom_id2] * r_epsr_table [distance_id];
desolv += (s1*v2 + s2*v1) * desolv_table [distance_id];
#if 0
el += q1q2[atom_id1][atom_id2] * r_epsr_table [distance_id];
desolv += (s1*v2 + s2*v1) * desolv_table [distance_id];
}
#endif
}
}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment