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carlocamillonicarlocamilloni
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Merge pull request #552 from carlocamilloni/main
more control over sigma ranges in both attractive and repulsive interactions
2 parents b1b8536 + c005e3d commit 6f3654f

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7 files changed

+2677
-2664
lines changed

7 files changed

+2677
-2664
lines changed

‎src/multiego/ensemble.py‎

Lines changed: 17 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -995,10 +995,10 @@ def set_sig_epsilon(meGO_LJ, parameters):
995995
)
996996
# higher value for repulsion
997997
meGO_LJ.loc[
998-
(meGO_LJ["1-4"] != "1_4") & (meGO_LJ["epsilon"] < 0.0) & (-meGO_LJ["epsilon"] > 50.0 * meGO_LJ["rep"]),
998+
(meGO_LJ["1-4"] != "1_4") & (meGO_LJ["epsilon"] < 0.0) & (-meGO_LJ["epsilon"] > 2.0 * meGO_LJ["rep"]),
999999
"epsilon",
10001000
] = (
1001-
-50.0 * meGO_LJ["rep"]
1001+
-2.0 * meGO_LJ["rep"]
10021002
)
10031003

10041004
# but within a lower
@@ -1010,14 +1010,27 @@ def set_sig_epsilon(meGO_LJ, parameters):
10101010
)
10111011
# and an upper value
10121012
meGO_LJ.loc[
1013-
(meGO_LJ["1-4"] == "1_4") & (-meGO_LJ["epsilon"] > 5.0 * meGO_LJ["rep"]),
1013+
(meGO_LJ["1-4"] == "1_4") & (-meGO_LJ["epsilon"] > 2.0 * meGO_LJ["rep"]),
10141014
"epsilon",
10151015
] = (
1016-
-5.0 * meGO_LJ["rep"]
1016+
-2.0 * meGO_LJ["rep"]
10171017
)
10181018

10191019
# Sigma is set from the estimated interaction length
10201020
meGO_LJ = meGO_LJ.assign(sigma=meGO_LJ["distance"] / 2 ** (1.0 / 6.0))
1021+
# sigma boundaries for attractive interactions
1022+
meGO_LJ.loc[
1023+
(meGO_LJ["1-4"] != "1_4") & (meGO_LJ["epsilon"] > 0.0) & (meGO_LJ["sigma"] < 0.7 * meGO_LJ["mg_sigma"]),
1024+
"sigma",
1025+
] = (
1026+
0.7 * meGO_LJ["mg_sigma"]
1027+
)
1028+
meGO_LJ.loc[
1029+
(meGO_LJ["1-4"] != "1_4") & (meGO_LJ["epsilon"] > 0.0) & (meGO_LJ["sigma"] > 1.3 * meGO_LJ["mg_sigma"]),
1030+
"sigma",
1031+
] = (
1032+
1.3 * meGO_LJ["mg_sigma"]
1033+
)
10211034

10221035
# for repulsive interaction we reset sigma to its effective value
10231036
# this because when merging repulsive contacts from different sources what will matters

‎test/test_outputs/abetaref/case_1/ffnonbonded.itp‎

Lines changed: 445 additions & 445 deletions
Large diffs are not rendered by default.

‎test/test_outputs/abetaref/case_1/topol_mego.top‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1723,9 +1723,9 @@ ABeta 3
17231723

17241724
[ pairs ]
17251725
; ai aj func c6 c12 ; probability rc_probability source
1726-
1 4 1 0.000000e+00 3.444458e-07 ; 0.899647 0.968846 native_MD
1726+
1 4 1 0.000000e+00 2.624179e-07 ; 0.899647 0.968846 native_MD
17271727
1 9 1 0.000000e+00 2.801444e-06 ; 1.000000 0.999999 native_MD
1728-
3 8 1 0.000000e+00 1.395276e-06 ; 1.000000 1.000000 native_MD
1728+
3 8 1 0.000000e+00 8.062625e-07 ; 1.000000 1.000000 native_MD
17291729
3 9 1 0.000000e+00 9.196800e-07 ; 0.999997 0.999995 native_MD
17301730
4 7 1 0.000000e+00 1.965490e-07 ; 0.965691 0.879256 native_MD
17311731
7 12 1 0.000000e+00 1.398918e-06 ; 0.999994 0.999996 native_MD
@@ -1770,7 +1770,7 @@ ABeta 3
17701770
64 67 1 0.000000e+00 2.733610e-07 ; 0.964336 0.888538 native_MD
17711771
67 72 1 0.000000e+00 1.057447e-06 ; 1.000000 0.999997 native_MD
17721772
67 74 1 0.000000e+00 1.674761e-06 ; 0.999999 1.000000 native_MD
1773-
69 73 1 0.000000e+00 1.408520e-07 ; 0.502425 0.786101 native_MD
1773+
69 73 1 0.000000e+00 1.153215e-07 ; 0.502425 0.786101 native_MD
17741774
69 76 1 0.000000e+00 3.477301e-07 ; 1.000000 0.999999 native_MD
17751775
72 75 1 0.000000e+00 3.093713e-07 ; 1.000000 1.000000 native_MD
17761776
72 76 1 0.000000e+00 1.652998e-06 ; 0.999996 1.000000 native_MD
@@ -1784,7 +1784,7 @@ ABeta 3
17841784
84 93 1 0.000000e+00 3.808673e-07 ; 0.999997 1.000000 native_MD
17851785
84 94 1 0.000000e+00 2.090282e-06 ; 1.000000 0.999991 native_MD
17861786
85 92 1 0.000000e+00 2.411157e-07 ; 0.975535 0.903955 native_MD
1787-
92 97 1 0.000000e+00 3.501368e-06 ; 1.000000 1.000000 native_MD
1787+
92 97 1 0.000000e+00 3.483679e-06 ; 1.000000 1.000000 native_MD
17881788
92 102 1 0.000000e+00 1.339602e-06 ; 1.000000 0.999997 native_MD
17891789
94 98 1 0.000000e+00 4.905859e-07 ; 0.999889 0.999271 native_MD
17901790
94 104 1 0.000000e+00 2.518661e-07 ; 1.000000 0.999992 native_MD
@@ -1890,11 +1890,11 @@ ABeta 3
18901890
228 233 1 0.000000e+00 2.786243e-07 ; 1.000000 0.999991 native_MD
18911891
231 236 1 0.000000e+00 1.180615e-06 ; 1.000000 1.000000 native_MD
18921892
231 238 1 0.000000e+00 1.592542e-06 ; 1.000000 1.000000 native_MD
1893-
233 237 1 0.000000e+00 1.412343e-07 ; 0.543234 0.780536 native_MD
1893+
233 237 1 0.000000e+00 1.153215e-07 ; 0.543234 0.780536 native_MD
18941894
233 240 1 0.000000e+00 3.100658e-07 ; 1.000000 0.999991 native_MD
18951895
236 239 1 0.000000e+00 2.900603e-07 ; 0.999999 0.999998 native_MD
18961896
236 240 1 0.000000e+00 1.713347e-06 ; 0.999998 1.000000 native_MD
1897-
237 238 1 0.000000e+00 1.790022e-07 ; 0.834778 0.734050 native_MD
1897+
237 238 1 0.000000e+00 1.781459e-07 ; 0.834778 0.734050 native_MD
18981898
238 243 1 0.000000e+00 1.795678e-06 ; 1.000000 0.999998 native_MD
18991899
238 247 1 0.000000e+00 1.345803e-06 ; 0.999995 0.999992 native_MD
19001900
240 244 1 0.000000e+00 1.134655e-07 ; 0.980936 0.878809 native_MD
@@ -1936,14 +1936,14 @@ ABeta 3
19361936
284 286 1 0.000000e+00 4.328398e-07 ; 0.999994 0.999057 native_MD
19371937
286 291 1 0.000000e+00 1.274385e-06 ; 1.000000 0.999999 native_MD
19381938
288 293 1 0.000000e+00 2.738835e-07 ; 1.000000 0.999995 native_MD
1939-
291 296 1 0.000000e+00 4.181428e-06 ; 0.999999 1.000000 native_MD
1939+
291 296 1 0.000000e+00 3.483679e-06 ; 0.999999 1.000000 native_MD
19401940
291 300 1 0.000000e+00 1.370842e-06 ; 0.999998 1.000000 native_MD
19411941
293 297 1 0.000000e+00 7.963006e-07 ; 1.000000 0.999995 native_MD
19421942
293 302 1 0.000000e+00 2.273010e-07 ; 1.000000 1.000000 native_MD
19431943
296 301 1 0.000000e+00 5.958435e-07 ; 1.000000 1.000000 native_MD
19441944
296 302 1 0.000000e+00 2.016641e-06 ; 1.000000 0.999998 native_MD
19451945
297 300 1 0.000000e+00 6.439820e-07 ; 1.000000 1.000000 native_MD
1946-
300 305 1 0.000000e+00 3.646540e-06 ; 0.999996 1.000000 native_MD
1946+
300 305 1 0.000000e+00 3.483679e-06 ; 0.999996 1.000000 native_MD
19471947
300 309 1 0.000000e+00 1.468976e-06 ; 0.999998 0.999997 native_MD
19481948
302 306 1 0.000000e+00 4.809207e-07 ; 0.999939 0.999213 native_MD
19491949
302 311 1 0.000000e+00 1.839234e-07 ; 1.000000 0.999992 native_MD

‎test/test_outputs/gpref/case_2/ffnonbonded.itp‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1697,7 +1697,7 @@ OE2_GB_1_Protein_56 8 15.9994 0.0 A 1.442372e-04 4.728253e-
16971697
OH_GB_1_Protein_3 C_GB_1_Protein_22 1 7.355385e-04 5.764939e-07 ; 0.303644 2.346152e-01 0.987501 5.383375e-04 0.004546 0.016805 True md_ensemble 27 188
16981698
OH_GB_1_Protein_3 O_GB_1_Protein_22 1 7.602929e-04 6.776040e-07 ; 0.310217 2.132681e-01 0.491460 5.192650e-04 0.004546 0.016806 True md_ensemble 27 189
16991699
OH_GB_1_Protein_3 N_GB_1_Protein_23 1 4.815354e-04 2.468155e-07 ; 0.282894 2.348681e-01 0.995697 3.220725e-04 0.004546 0.016806 True md_ensemble 27 190
1700-
OH_GB_1_Protein_3 H_GB_1_Protein_23 1 1.555026e-04 2.927638e-08 ; 0.239403 2.064895e-01 0.393783 7.637000e-05 0.004546 0.000461 True md_ensemble 27 191
1700+
OH_GB_1_Protein_3 H_GB_1_Protein_23 1 9.454452e-05 1.082218e-08 ; 0.220350 2.064895e-01 0.393783 7.637000e-05 0.004546 0.000461 True md_ensemble 27 191
17011701
OH_GB_1_Protein_3 CA_GB_1_Protein_23 1 1.009284e-03 1.083713e-06 ; 0.320000 2.349916e-01 0.999726 1.288255e-03 0.004546 0.011923 True md_ensemble 27 192
17021702
OH_GB_1_Protein_3 CB_GB_1_Protein_23 1 1.108736e-03 1.310986e-06 ; 0.325183 2.344219e-01 0.981280 1.286520e-03 0.004546 0.016804 True md_ensemble 27 193
17031703
OH_GB_1_Protein_3 H_GB_1_Protein_24 1 1.043448e-05 2.474509e-10 ; 0.169500 1.100000e-01 1.000000 1.000000e+00 1.000000 1.000000 False mg 27 197
@@ -13690,7 +13690,7 @@ OG1_GB_1_Protein_44 H_GB_1_Protein_50 1 1.043448e-05 2.474509e-10 ; 0.1695
1369013690
OG1_GB_1_Protein_44 H_GB_1_Protein_51 1 1.043448e-05 2.474509e-10 ; 0.169500 1.100000e-01 1.000000 1.000000e+00 1.000000 1.000000 False mg 378 438
1369113691
OG1_GB_1_Protein_44 H_GB_1_Protein_52 1 1.043448e-05 2.474509e-10 ; 0.169500 1.100000e-01 1.000000 1.000000e+00 1.000000 1.000000 False mg 378 446
1369213692
OG1_GB_1_Protein_44 N_GB_1_Protein_53 1 1.455043e-03 3.306979e-06 ; 0.362598 1.600516e-01 0.086300 1.530500e-04 0.004546 0.016806 True md_ensemble 378 457
13693-
OG1_GB_1_Protein_44 H_GB_1_Protein_53 1 7.450697e-05 1.669988e-08 ; 0.246464 8.310373e-02 0.006976 3.471500e-05 0.004546 0.000461 True md_ensemble 378 458
13693+
OG1_GB_1_Protein_44 H_GB_1_Protein_53 1 3.805037e-05 4.355492e-09 ; 0.220350 8.310373e-02 0.006976 3.471500e-05 0.004546 0.000461 True md_ensemble 378 458
1369413694
OG1_GB_1_Protein_44 CA_GB_1_Protein_53 1 2.308351e-03 6.900237e-06 ; 0.379542 1.930544e-01 0.253821 7.056275e-04 0.004546 0.011923 True md_ensemble 378 459
1369513695
OG1_GB_1_Protein_44 CB_GB_1_Protein_53 1 1.007418e-03 1.206402e-06 ; 0.325872 2.103134e-01 0.446213 1.630037e-03 0.004546 0.011923 True md_ensemble 378 460
1369613696
OG1_GB_1_Protein_44 OG1_GB_1_Protein_53 1 2.349088e-04 8.893348e-08 ; 0.268964 1.551220e-01 0.073456 7.636750e-04 0.004546 0.016806 True md_ensemble 378 461

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