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Commit f25db674 authored by peastman's avatar peastman
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Converted GBn and GBn2 to use discrete functions (improves performance)

parent 75a04e7f
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wrappers/python/simtk/openmm/app/internal/customgbforces.py
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...@@ -6,9 +6,9 @@ Simbios, the NIH National Center for Physics-Based Simulation of ...@@ -6,9 +6,9 @@ Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org. Medical Research, grant U54 GM072970. See https://simtk.org.
Portions copyright (c) 2012 University of Virginia and the Authors. Portions copyright (c) 2012-2014 University of Virginia and the Authors.
Authors: Christoph Klein, Michael R. Shirts Authors: Christoph Klein, Michael R. Shirts
Contributors: Jason M. Swails Contributors: Jason M. Swails, Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"), copy of this software and associated documentation files (the "Software"),
...@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE. ...@@ -31,7 +31,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
from __future__ import division from __future__ import division
from simtk.openmm import CustomGBForce from simtk.openmm import CustomGBForce, Discrete1DFunction
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444, d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196, 2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
...@@ -331,8 +331,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -331,8 +331,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addGlobalParameter("neckScale", 0.361825) custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68) custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440) custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addFunction("getm0", m0, 0, 440) custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;" custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);" "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
...@@ -380,8 +380,8 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -380,8 +380,8 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom.addGlobalParameter("neckScale", 0.826836) custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68) custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440) custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addFunction("getm0", m0, 0, 440) custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
custom.addComputedValue("I", "Ivdw+neckScale*Ineck;" custom.addComputedValue("I", "Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);" "Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
......
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