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Commit 37787af9 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1540 from peastman/gbnerror 

Fixed nan with GBn and GBn2
parents ac8452c7 162f5cc7
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wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 37787af9
...@@ -760,7 +760,7 @@ class GBSAGBnForce(CustomAmberGBForceBase): ...@@ -760,7 +760,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
self.addComputedValue("I", "Ivdw+neckScale*Ineck;" self.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+" "Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+"
"0.3*1000000*(r-getd0(radindex1,radindex2))^6);" "0.3*1000000*(r-getd0(radindex1,radindex2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" "Ivdw=select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2);"
...@@ -851,7 +851,7 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -851,7 +851,7 @@ class GBSAGBn2Force(GBSAGBnForce):
self.addComputedValue("I", "Ivdw+neckScale*Ineck;" self.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+" "Ineck=step(radius1+radius2+neckCut-r)*getm0(radindex1,radindex2)/(1+100*(r-getd0(radindex1,radindex2))^2+"
"0.3*1000000*(r-getd0(radindex1,radindex2))^6);" "0.3*1000000*(r-getd0(radindex1,radindex2))^6);"
"Ivdw=step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);" "Ivdw=select(step(r+sr2-or1), 0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r), 0);"
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2);"
......
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