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jayponderjayponder
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enable rigid 4-site water in Cartesian minimization & MD
1 parent 1323107 commit 2b9e9f9

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‎example/tip4pbox.key‎

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echo ###################################################################
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echo ## MD Simulation of TIP4P requires special constraint handling ##
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echo ## (see source file "beeman.4site" in the /other subdirectory) ##
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echo ###################################################################
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parameters ../params/oplsaa08
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#verbose
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‎params/0README‎

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@@ -56,6 +56,9 @@
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modification of 2018 parameters from the Varma group
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reworks many parameters involving ion interactions.
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amoebail Ionic liquid parameters for the AMOEBA force field as
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provided by Andres Cisneros at Univ. Texas at Dallas
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amoebanuc Nucleic acid parameter for the AMOEBA polarizable atomic
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multipole force field. The 2017 version is provided.
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@@ -134,17 +137,21 @@
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greater bias toward planarity at many types of trigonal
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nitrogan such as amides, ureas, anilines, etc.
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oplsaa OPLS-AA from July 2008 with all-atom parameters for
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proteins, nucleic acids and many general classes of
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oplsaa08 OPLS-AA parameters from July 2008 with all-atom parameters
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for proteins, nucleic acids and many general classes of
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organic molecules.
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oplsaa24 OPLS-AA parameters based on results for a series of small
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organic molecules generated by the LigParGen server, and
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modified to provide transferable functional group values.
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oplsaal A modified version of the 1997 OPLS-AA with optimized
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torsional parameters for the protein backbone and side
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chains as published in 2001.
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oplsua OPLS-UA containing united-atom parameters for proteins
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and many classes of organic molecules. Explicit hydrogens
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on polar atoms and aromatic carbons.
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oplsua97 OPLS-UA containing united-atom parameters from 1997 for
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proteins and many types of organic molecules. Explicit
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hydrogens on polar atoms and aromatic carbons.
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smoothaa Parameters for use with the Tinker potential energy
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smoothing methods. Based on the OPLS-AA parameters, but
@@ -162,8 +169,10 @@
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fit to cluster data and a number of liquid properties
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using the Force Balance optimization method.
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water19 Initial unpublished parameters for a HIPPO water model
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fit to clusters, liquid properties and ice without and
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charge flux terms.
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water21 Final HIPPO water parameters including charge flux terms,
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as published in 2021.
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water21 Final HIPPO water parameters including charge flux terms.
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water22 An update of the AMOEBA 2003 water model derived by
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Chengwen Liu at Univ. of Texas-Austin. Tuned parameters
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are vdw and bond/angle constants, the model provides
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good agreement with experiment and high-quality QM data.

‎params/amber14sb.prm‎

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@@ -32,14 +32,14 @@ and Backbone Parameters from ff99SB, J. Chem. Theory Comput., 11, 2696-2713
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(2015) [Protein ff14SB]
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R. Galindo-Murillo, J. C. Robertson, M. Zgarbovic, J. Sponer, M. Otyepka,
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P. Jureska, T. E. Cheatham, Assessing the Current State of Amber Force
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P. Jureska and T. E. Cheatham, Assessing the Current State of Amber Force
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Field Modifications for DNA. J. Chem. Theory Comput., 12, 4114–4127 (2016)
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[DNA OL15]
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M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham,
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P. Jurecka, Refinement of the Cornell et al. Nucleic Acids Force Field
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Based on Reference Quantum Chemical Calculations of Glycosidic Torsion
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Profiles, J. Chem. Theory Comput., 7, 2886–2902 (2011) [RNA OL3]
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M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham
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and P. Jurecka, Refinement of the Cornell et al. Nucleic Acids Force
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Field Based on Reference Quantum Chemical Calculations of Glycosidic
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Torsion Profiles, J. Chem. Theory Comput., 7, 2886–2902 (2011) [RNA OL3]
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Current parameter values are available in the AmberTools package, which
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is downloadable from http://ambermd.org/

‎params/basic.prm‎

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@@ -190,6 +190,7 @@ bond 64 351 150.00 1.9500
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bond 64 531 150.00 2.1600
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bond 72 72 550.00 1.3200
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bond 72 73 550.00 1.3100
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bond 72 164 380.00 1.6900
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bond 73 73 550.00 1.3700
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bond 73 81 550.00 1.2200
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bond 73 154 380.00 1.6800
@@ -223,6 +224,7 @@ angle 11 63 64 35.00 120.00
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angle 11 63 72 35.00 120.00
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angle 11 63 73 35.00 120.00
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angle 11 63 74 35.00 120.00
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angle 11 63 81 35.00 120.00
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angle 11 63 82 45.00 120.00
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angle 11 63 91 60.00 120.00
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angle 11 63 162 30.00 120.00
@@ -317,6 +319,7 @@ angle 63 72 63 70.00 120.00
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angle 63 72 64 50.00 120.00
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angle 63 72 72 70.00 108.20
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angle 63 72 73 70.00 120.00
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angle 63 72 164 55.00 120.00
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angle 72 72 73 70.00 108.80
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angle 11 73 11 45.00 109.50
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angle 11 73 63 35.00 120.00
@@ -363,10 +366,12 @@ angle 63 162 63 50.00 98.50
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angle 63 162 64 50.00 98.00
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angle 64 162 64 50.00 96.00
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angle 64 162 162 85.00 103.00
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angle 63 164 72 75.00 101.10
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angle 63 164 73 75.00 101.10
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angle 63 164 81 75.00 103.00
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angle 64 164 73 75.00 101.10
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angle 64 164 81 75.00 103.00
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angle 72 164 81 70.00 108.80
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angle 73 164 81 70.00 108.80
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angle 81 164 81 65.00 114.00
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@@ -413,6 +418,7 @@ torsion 0 64 162 0 0.300 0.0 3
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torsion 0 64 164 0 0.300 0.0 3
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torsion 0 72 72 0 10.000 180.0 2
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torsion 0 72 73 0 7.000 180.0 2
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torsion 0 72 164 0
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torsion 0 73 73 0 5.000 180.0 2
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torsion 0 73 154 0
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torsion 0 73 164 0

‎params/oplsaal.prm‎

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@@ -14,8 +14,8 @@ radiusrule GEOMETRIC
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radiustype SIGMA
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radiussize DIAMETER
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epsilonrule GEOMETRIC
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torsionunit 0.5
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imptorunit 0.5
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torsionunit 0.5
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vdw-14-scale 2.0
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chg-14-scale 2.0
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electric 332.06
@@ -44,12 +44,6 @@ group of Prof. Karl F. Freed, Department of Chemistry, University
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of Chicago by modifying the Tinker OPLS-AA parameters as per the
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Kaminsky, et al. article cited above
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Some parameters distributed with Tinker are from "OPLS and OPLS-AA
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Parameters for Organic Molecules, Ions, and Nucleic Acids" as provided
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by W. L. Jorgensen, Yale University, October 1997. These values have
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been updated in the Tinker version based on subsequent publications
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from the Jorgensen Lab.
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#############################
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## ##

‎params/oplsua.prm‎

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##############################
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forcefield OPLS-UA
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forcefield OPLS-UA-1997
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vdwindex CLASS
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vdwtype LENNARD-JONES
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radiusrule GEOMETRIC
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radiustype SIGMA
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radiussize DIAMETER
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epsilonrule GEOMETRIC
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imptorunit 1.0
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torsionunit 1.0
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vdw-14-scale 8.0
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chg-14-scale 2.0
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electric 332.06

‎params/smoothua.prm‎

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@@ -15,6 +15,7 @@ radiusrule GEOMETRIC
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radiustype SIGMA
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radiussize DIAMETER
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epsilonrule GEOMETRIC
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torsionunit 1.0
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vdw-14-scale 8.0
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chg-14-scale 2.0
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electric 332.06

‎source/baoab.f‎

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@@ -36,12 +36,14 @@ subroutine baoab (istep,dt)
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implicit none
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integer i,j,k
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integer istep
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integer ia,ib,ic,id
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integer nrattle
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real*8 dt,dtr
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real*8 dt_2,dt_4
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real*8 etot,epot
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real*8 eksum
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real*8 temp,pres
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real*8 oterm,hterm
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real*8 ekin(3,3)
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real*8 stress(3,3)
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real*8, allocatable :: xold(:)
@@ -136,6 +138,23 @@ subroutine baoab (istep,dt)
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c
137139
call gradient (epot,derivs)
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c
141+
c distribute forces on any four-site water extra centers
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c
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do i = 1, nwat4
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ia = iwat4(1,i)
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ib = iwat4(2,i)
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ic = iwat4(3,i)
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id = iwat4(4,i)
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oterm = kwat4(1,i)
149+
hterm = kwat4(2,i)
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do j = 1, 3
151+
derivs(j,ib) = derivs(j,ib) + oterm*derivs(j,ia)
152+
derivs(j,ic) = derivs(j,ic) + hterm*derivs(j,ia)
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derivs(j,id) = derivs(j,id) + hterm*derivs(j,ia)
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derivs(j,ia) = 0.0d0
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end do
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end do
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c
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c use Newton's second law to get the next accelerations;
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c find the full-step velocities using the Verlet recursion
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c

‎source/beeman.f‎

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@@ -39,11 +39,13 @@ subroutine beeman (istep,dt)
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implicit none
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integer i,j,k
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integer istep
42+
integer ia,ib,ic,id
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real*8 dt,dt_x,factor
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real*8 etot,eksum,epot
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real*8 temp,pres
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real*8 part1,part2
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real*8 dt_2,term
48+
real*8 oterm,hterm
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real*8 ekin(3,3)
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real*8 stress(3,3)
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real*8, allocatable :: xold(:)
@@ -105,6 +107,23 @@ subroutine beeman (istep,dt)
105107
c
106108
call gradient (epot,derivs)
107109
c
110+
c distribute forces on any four-site water extra centers
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c
112+
do i = 1, nwat4
113+
ia = iwat4(1,i)
114+
ib = iwat4(2,i)
115+
ic = iwat4(3,i)
116+
id = iwat4(4,i)
117+
oterm = kwat4(1,i)
118+
hterm = kwat4(2,i)
119+
do j = 1, 3
120+
derivs(j,ib) = derivs(j,ib) + oterm*derivs(j,ia)
121+
derivs(j,ic) = derivs(j,ic) + hterm*derivs(j,ia)
122+
derivs(j,id) = derivs(j,id) + hterm*derivs(j,ia)
123+
derivs(j,ia) = 0.0d0
124+
end do
125+
end do
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c
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c make half-step temperature and pressure corrections
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c
110129
call temper2 (dt,temp)

‎source/bussi.f‎

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@@ -39,13 +39,15 @@ subroutine bussi (istep,dt)
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implicit none
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integer i,j,k
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integer istep
42+
integer ia,ib,ic,id
4243
real*8 dt,dt_2,dt_x
4344
real*8 dt2_2,dt3_2
4445
real*8 epot,etot,eksum
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real*8 expterm,sinhterm
4647
real*8 kt,w,temp,pres
4748
real*8 part1,part2
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real*8 factor,term
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real*8 oterm,hterm
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real*8 ekin(3,3)
5052
real*8 stress(3,3)
5153
real*8, allocatable :: xold(:)
@@ -144,6 +146,23 @@ subroutine bussi (istep,dt)
144146
c
145147
call gradient (epot,derivs)
146148
c
149+
c distribute forces on any four-site water extra centers
150+
c
151+
do i = 1, nwat4
152+
ia = iwat4(1,i)
153+
ib = iwat4(2,i)
154+
ic = iwat4(3,i)
155+
id = iwat4(4,i)
156+
oterm = kwat4(1,i)
157+
hterm = kwat4(2,i)
158+
do j = 1, 3
159+
derivs(j,ib) = derivs(j,ib) + oterm*derivs(j,ia)
160+
derivs(j,ic) = derivs(j,ic) + hterm*derivs(j,ia)
161+
derivs(j,id) = derivs(j,id) + hterm*derivs(j,ia)
162+
derivs(j,ia) = 0.0d0
163+
end do
164+
end do
165+
c
147166
c use Newton's second law to get the next accelerations
148167
c
149168
do i = 1, nuse

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