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Revert "revert more general doc changes. those are moved to a separate branch for further edits."

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This reverts commit fb9ae23516.
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Axel Kohlmeyer
2024-01-18 18:14:41 -05:00
parent 54794a45de
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@ -60,3 +60,4 @@ src/Makefile.package.settings-e
/cmake/build/x64-Debug-Clang
/install/x64-GUI-MSVC
/install
.Rhistory

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doc/src/Howto_bioFF.rst
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@ -11,12 +11,30 @@ commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
output into LAMMPS input. LAMMPS input scripts can also be generated by `charmm-gui.org <https://charmm-gui.org/>`_.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
CHARMM and AMBER
----------------
The `CHARMM force field <https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref:`(MacKerell) <howto-MacKerell>` and `AMBER force field <https://ambermd.org/AmberModels.php>`_ :ref:`(Cornell) <howto-Cornell>` have potential energy function of the form
.. math::
V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
\text{charmm} \\
\text{charmmfsw}
}} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
& \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
\text{lj/charmm/coul/charmm} \\
\text{lj/charmm/coul/charmm/implicit} \\
\text{lj/charmm/coul/long} \\
\text{lj/charmm/coul/msm} \\
\text{lj/charmmfsw/coul/charmmfsh} \\
\text{lj/charmmfsw/coul/long}
}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
The terms are computed by bond styles (relationship between 2 atoms), angle styles (between 3 atoms) , dihedral/improper styles (between 4 atoms), pair styles (non-covalently bonded pair interactions) and special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for details) corrects for pairs of dihedral angles ("Correction MAP") to significantly improve the structural and dynamic properties of proteins in crystalline and solution environments :ref:`(Brooks) <howto-Brooks>`. The AMBER force field does not include the CMAP term.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -31,10 +49,61 @@ command's documentation for the formula it computes.
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
* :doc:`special_bonds <special_bonds>` charmm
* :doc:`special_bonds <special_bonds>` amber
The pair styles compute Lennard Jones (LJ) and Coulombic interactions with additional switching or shifting functions that ramp the energy and/or force smoothly to zero between an inner :math:`(a)` and outer :math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their name compute the LJ and Coulombic interactions with an energy switching function (esw) S(r) which ramps the energy smoothly to zero between the inner and outer cutoff. This can cause irregularities in pairwise forces (due to the discontinuous second derivative of energy at the boundaries of the switching region), which in some cases can result in complications in energy minimization and detectable artifacts in MD simulations.
.. math::
LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
S(r) &= \frac{ \left(b^2 - r^2\right)^2
\left(b^2 + 2r^2 - 3{a^2}\right)}
{ \left(b^2 - a^2\right)^3 }\\[.6em]
E_{LJ}(r) &= \begin{cases}
LJ(r), & r \leq a \\
LJ(r) S(r), & a < r \leq b \\
0, &r > b
\end{cases} \\[.6em]
E_{coul}(r) &= \begin{cases}
C(r), & r \leq a \\
C(r) S(r), & a < r \leq b \\
0, & r > b
\end{cases}
.. image:: img/howto_charmm_ELJ.png
:align: center
|
The newer styles with *charmmfsw* or *charmmfsh* in their name replace energy switching with force switching (fsw) for LJ interactions and force shifting (fsh) functions for Coulombic interactions :ref:`(Steinbach) <howto-Steinbach>`
.. math::
E_{LJ}(r) = & \begin{cases}
4 \epsilon \sigma^6 \left(\frac{\displaystyle\sigma
^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
\frac{\displaystyle 4 \epsilon \sigma^6 \left(\sigma ^6
\left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
\left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
\left(b^6-a^6\right)} & a<r \leq b\\
0, & r>b
\end{cases}\\[.6em]
E_{coul}(r) & = \begin{cases}
C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, & r \leq b \\
0, & r > b
\end{cases}
.. image:: img/howto_charmmfsw_ELJ.png
:align: center
|
These styles are used by LAMMPS input scripts generated by `charmm-gui.org <https://charmm-gui.org/>`_ :ref:`(Brooks) <howto-Brooks>`. A `minimal PDB example 1HVN <https://www.rcsb.org/structure/1HVN>`_ with at least one protein segment, at least one DNA segment, and no modified engineered residues is available in the ``lammps/examples/charmm/1hvn`` directory. A better example is `PDB 2CV5 <https://www.rcsb.org/structure/2CV5>`_ with size too big to include in lammps examples, which is left as an exercise to the reader (go to charmm-gui.org and type in 2CV5 in PDB field of Solution Builder to generate LAMMPS scripts to simulate a solvated human nucleosome with histone octamer and dsDNA wrapped around it).
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
@ -43,9 +112,16 @@ command's documentation for the formula it computes.
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages.
.. note::
TIP3P water model MUST be used with CHARMM force field not TIP4P, TIP5P or SPC. In fact, `"using the SPC model with CHARMM parameters is a bad idea" <https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to enable TIP4P style water in CHARMM, you would have to write a new pair style" <https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_ . LAMMPS input scripts generated by Solution Builder on charmm-gui.org use TIP3P molecules for solvation. Any other water model can and probably will lead to false conclusions.
COMPASS
-------
COMPASS is a general force field for atomistic simulation of common
organic molecules, inorganic small molecules, and polymers which was
developed using ab initio and empirical parameterization techniques.
developed using ab initio and empirical parameterization techniques :ref:`(Sun) <howto-Sun>`.
See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA's Materials Studio
files. Please note that the msi2lmp tool is very old and largely
@ -70,6 +146,9 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
DREIDING
--------
DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
predicting structures and dynamics of organic, biological and main-group
inorganic molecules. The philosophy in DREIDING is to use general force
@ -113,18 +192,25 @@ documentation for the formula it computes.
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
Fischer, Gao, Guo, Ha, et al (1998). All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f
.. _howto-Cornell:
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
Spellmeyer, Fox, Caldwell, Kollman (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002
.. _howto-Steinbach:
**(Steinbach)** Steinbach, Brooks (1994). New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702
.. _howto-Brooks:
**(Brooks)** Brooks, et al (2009). CHARMM: The biomolecular simulation program. J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287
.. _howto-Sun:
**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Sun)** Sun (1998). COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds. J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v
.. _howto-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
**(Mayo)** Mayo, Olfason, Goddard III (1990). DREIDING: a generic force field for molecular simulations. J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010

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@ -112,26 +112,22 @@ Description
These pair styles compute Lennard Jones (LJ) and Coulombic
interactions with additional switching or shifting functions that ramp
the energy and/or force smoothly to zero between an inner and outer
cutoff. They are implementations of the widely used CHARMM force
field used in the `CHARMM <https://www.charmm.org>`_ MD code (and
others). See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
CHARMM force field.
cutoff. They implement the widely used CHARMM force field, see
:doc:`Howto discussion on biomolecular force fields <Howto_bioFF>` for
details.
The styles with *charmm* (not *charmmfsw* or *charmmfsh*\ ) in their
name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
shown in the formula below as S(r)), which ramps the energy smoothly
to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.
LJ and Coulombic interactions with an energy switching function which
ramps the energy smoothly to zero between the inner and outer cutoff.
This can cause irregularities in pairwise forces (due to the discontinuous
second derivative of energy at the boundaries of the switching region),
which in some cases can result in detectable artifacts in an MD simulation.
The newer styles with *charmmfsw* or *charmmfsh* in their name replace
the energy switching with force switching (fsw) and force shifting
(fsh) functions, for LJ and Coulombic interactions respectively.
These follow the formulas and description given in
:ref:`(Steinbach) <Steinbach>` and :ref:`(Brooks) <Brooks1>` to minimize these
artifacts.
.. note::
@ -152,26 +148,6 @@ artifacts.
the CHARMM force field energies and forces, when using one of these
two CHARMM pair styles.
.. math::
E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
= & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
= & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] \\
C(r) = & \frac{C q_i q_j}{ \epsilon r} \\
S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
\left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
{ \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
where S(r) is the energy switching function mentioned above for the
*charmm* styles. See the :ref:`(Steinbach) <Steinbach>` paper for the
functional forms of the force switching and force shifting functions
used in the *charmmfsw* and *charmmfsh* styles.
When using the *lj/charmm/coul/charmm styles*, both the LJ and
Coulombic terms require an inner and outer cutoff. They can be the
same for both formulas or different depending on whether 2 or 4

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@ -0,0 +1,340 @@
#CMAP for C NH1 CT1 C NH1 CT1 C NH1; id=1
#phi = -180.000000
0.130000 0.770000 0.970000 1.250000 2.120000
2.720000 2.090000 1.790000 0.780000 -0.690000
1.000000 -2.200000 -4.830000 -4.820000 -4.910000
-3.590000 -2.770000 -2.780000 -2.450000 -2.350000
-2.340000 -1.520000 -0.950000 -0.040000
#phi = -165.000000
-0.130000 1.380000 1.580000 1.870000 2.400000
2.490000 2.440000 1.930000 1.090000 0.640000
0.260000 -2.800000 -4.010000 -4.140000 -3.420000
-2.600000 -2.300000 -1.500000 -1.100000 -0.860000
-0.640000 -0.210000 -1.080000 -1.120000
#phi = -150.000000
0.080000 1.420000 1.620000 2.050000 2.650000
2.720000 2.320000 1.990000 1.560000 2.460000
-0.230000 -1.820000 -2.580000 -3.010000 -2.550000
-1.890000 -1.350000 -0.730000 0.070000 -0.230000
-0.770000 -1.280000 -1.290000 -0.820000
#phi = -135.000000
0.930000 1.520000 2.240000 2.550000 3.110000
2.920000 2.460000 2.190000 2.060000 1.850000
0.120000 -1.180000 -2.000000 -2.280000 -1.960000
-1.340000 -0.930000 0.020000 0.310000 -0.520000
-1.150000 -0.980000 -0.570000 -0.440000
#phi = -120.000000
1.360000 1.960000 2.700000 3.040000 3.700000
3.560000 2.640000 2.770000 2.720000 1.630000
0.710000 -0.790000 -2.120000 -2.630000 -1.800000
-0.430000 -0.060000 0.440000 0.910000 -0.550000
-0.970000 -0.860000 -0.250000 0.450000
#phi = -105.000000
2.050000 2.540000 2.820000 3.090000 3.370000
3.550000 3.070000 2.900000 2.960000 2.120000
0.910000 -0.820000 -2.090000 -2.240000 -1.460000
0.210000 0.080000 0.770000 1.040000 -0.120000
-0.320000 -0.160000 0.310000 0.730000
#phi = -90.000000
1.450000 2.750000 2.740000 3.160000 3.450000
3.340000 3.180000 3.900000 3.340000 2.440000
0.910000 -0.610000 -1.510000 -1.620000 -0.960000
-0.020000 0.420000 0.910000 0.460000 0.150000
-0.070000 0.020000 0.280000 0.750000
#phi = -75.000000
1.380000 3.350000 2.350000 3.060000 3.810000
3.700000 3.580000 4.210000 3.540000 1.690000
0.100000 -0.680000 -0.120000 -0.430000 -0.600000
0.230000 0.420000 0.300000 0.550000 0.190000
-0.250000 -0.190000 -0.250000 0.470000
#phi = -60.000000
0.240000 1.230000 1.720000 3.170000 4.210000
4.390000 4.280000 3.670000 2.270000 -0.480000
-0.410000 -0.040000 -0.360000 -0.820000 -0.170000
0.140000 0.270000 0.320000 0.310000 -0.670000
-0.950000 -1.530000 -1.480000 -0.200000
#phi = -45.000000
-1.180000 0.080000 2.350000 4.210000 5.380000
5.390000 4.380000 2.460000 1.120000 0.110000
0.010000 -0.150000 -0.800000 -0.580000 0.080000
0.270000 -0.050000 0.380000 0.250000 -0.890000
-1.580000 -1.950000 -1.980000 -2.000000
#phi = -30.000000
-1.170000 1.070000 4.180000 6.740000 6.070000
4.810000 2.780000 1.320000 0.770000 -0.010000
0.280000 -0.710000 1.310000 1.520000 1.920000
2.220000 0.190000 0.530000 0.330000 -1.600000
-2.850000 -3.550000 -3.280000 -2.660000
#phi = -15.000000
0.290000 5.590000 3.730000 3.220000 3.270000
2.520000 1.590000 1.380000 0.860000 0.660000
1.620000 0.850000 0.510000 0.740000 1.020000
1.620000 -0.340000 0.180000 -0.610000 -2.560000
-3.790000 -3.810000 -3.160000 -1.750000
#phi = 0.000000
2.830000 0.790000 0.320000 0.480000 0.630000
0.980000 1.240000 1.670000 1.650000 2.520000
1.610000 0.780000 0.120000 0.070000 0.120000
-1.570000 -1.210000 -1.930000 -2.600000 -3.790000
-3.930000 -3.620000 -2.680000 -0.920000
#phi = 15.000000
-0.780000 -1.910000 -2.050000 -1.850000 -1.050000
0.180000 1.680000 2.220000 1.360000 2.450000
1.440000 0.680000 -0.240000 -0.540000 -0.790000
-2.180000 -3.210000 -4.350000 -3.940000 -3.910000
-3.460000 -2.770000 1.760000 0.310000
#phi = 30.000000
-2.960000 -3.480000 -3.440000 -2.400000 -1.130000
0.340000 1.430000 1.390000 0.970000 2.460000
1.520000 0.550000 -0.410000 -1.480000 -3.580000
-4.130000 -4.560000 -4.440000 -3.580000 -2.960000
-1.960000 -1.070000 -1.600000 -2.450000
#phi = 45.000000
-4.020000 -3.840000 -3.370000 -2.330000 -0.980000
0.360000 0.810000 0.750000 0.500000 1.900000
0.770000 -0.420000 -3.290000 -3.910000 -4.520000
-4.890000 -3.850000 -4.150000 -2.670000 -2.370000
-2.860000 -3.420000 -3.670000 -3.600000
#phi = 60.000000
-3.350000 -2.980000 -2.320000 -1.240000 -0.260000
0.720000 0.670000 0.440000 2.400000 1.630000
-2.010000 -3.310000 -3.990000 -4.530000 -4.850000
-3.770000 -3.940000 -3.890000 -2.610000 -3.510000
-3.760000 -3.640000 -3.450000 -3.340000
#phi = 75.000000
-2.250000 -1.640000 -1.010000 0.040000 0.640000
0.820000 0.520000 -0.010000 -0.370000 -1.190000
-2.390000 -3.380000 -4.500000 -5.590000 -5.510000
-4.940000 -3.830000 -3.840000 -3.700000 -4.150000
-4.170000 -3.730000 -3.740000 -2.620000
#phi = 90.000000
-1.720000 -1.180000 -0.430000 0.280000 0.810000
0.800000 0.480000 -0.340000 -0.790000 -1.770000
-2.810000 -3.800000 -5.220000 -6.280000 -6.580000
-5.640000 -5.060000 -4.020000 -4.150000 -4.470000
-4.100000 -3.770000 -3.160000 -2.650000
#phi = 105.000000
-1.850000 -1.090000 -0.450000 0.130000 1.010000
0.880000 0.490000 -0.220000 -0.860000 -1.680000
-3.010000 -4.130000 -5.990000 -6.860000 -6.830000
-5.850000 -3.860000 -4.860000 -4.910000 -4.720000
-4.600000 -4.090000 -3.270000 -2.410000
#phi = 120.000000
-1.970000 -1.120000 -0.540000 -0.150000 0.760000
1.040000 0.760000 0.310000 -0.330000 -1.870000
-3.370000 -5.010000 -6.120000 -7.050000 -6.980000
-3.700000 -4.510000 -5.090000 -5.420000 -4.850000
-4.440000 -4.000000 -3.420000 -2.750000
#phi = 135.000000
-2.110000 -1.170000 -0.320000 -0.010000 0.320000
1.090000 0.940000 0.630000 -0.170000 -1.830000
-3.470000 -4.950000 -6.110000 -1.920000 -4.050000
-5.000000 -5.000000 -4.840000 -4.890000 -4.300000
-4.490000 -4.440000 -4.160000 -3.180000
#phi = 150.000000
-1.760000 -0.400000 0.020000 0.360000 0.630000
1.260000 1.360000 0.950000 -0.070000 -1.480000
-3.150000 1.840000 -1.760000 -5.090000 -5.740000
-5.390000 -4.780000 -4.190000 -4.120000 -4.040000
-4.130000 -4.030000 -4.030000 -2.940000
#phi = 165.000000
-0.810000 -0.070000 0.380000 0.540000 1.280000
1.640000 1.700000 1.520000 0.630000 -1.090000
-2.740000 -0.740000 -4.560000 -6.410000 -5.890000
-5.140000 -4.190000 -3.670000 -3.840000 -3.560000
-3.550000 -3.250000 -2.750000 -1.810000
#CMAP for C NH1 CT2 C NH1 CT2 C NH1; id=2
#phi = -180.000000
0.235350 0.182300 0.177200 0.396800 0.859400
1.489700 2.092500 2.297700 1.808600 0.696200
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
0.696200 1.808200 2.301700 2.092600 1.489100
0.859500 0.396900 0.176900 0.182400
#phi = -165.000000
0.020100 -0.203800 -0.269700 0.014200 0.620800
1.392400 2.046200 2.188200 1.683900 0.688500
-0.373700 -0.703500 0.837800 3.704000 -0.730100
0.594100 1.713100 2.205800 2.026400 1.529800
1.027400 0.623800 0.348400 0.182800
#phi = -150.000000
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
1.168000 1.641000 1.618100 1.302200 0.615100
0.065700 0.738500 2.959500 -2.036600 -0.934600
0.407900 1.517000 1.984800 1.833100 1.435200
0.995600 0.562200 0.150600 -0.209000
#phi = -135.000000
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
0.454400 0.737600 0.879300 0.850100 0.670300
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
0.279600 1.322000 1.668300 1.521300 1.193900
0.765300 0.246000 -0.315500 -0.823200
#phi = -120.000000
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
-0.401000 -0.015100 0.321300 0.634600 0.976300
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
0.308700 1.098100 1.245300 1.133600 0.881800
0.448200 -0.153900 -0.823700 -1.404300
#phi = -105.000000
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
-0.980600 -0.429100 0.144700 0.734000 -0.918300
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
0.107000 0.496000 0.553500 0.584300 0.494000
0.098300 -0.529800 -1.237900 -1.840100
#phi = -90.000000
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
-0.439600 -1.038600 -1.741000 -2.373200
#phi = -75.000000
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
-1.360700 -2.009200 -2.745700 -3.424900
#phi = -60.000000
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
-0.174700 0.262600 0.039200 -0.663000 -1.530700
-2.478200 -3.465600 -4.334200 -5.011200
#phi = -45.000000
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
0.768200 0.568500 -0.831300 -2.343900 -3.037100
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
0.077000 0.441500 0.257500 -0.491100 -1.820600
-3.473100 -4.895200 -5.790700 -6.205900
#phi = -30.000000
-5.258225 -3.675795 -1.631110 0.430085 1.496470
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
0.054300 0.497200 0.599600 -0.171000 -2.137600
-4.237000 -5.584100 -6.135100 -6.067000
#phi = -15.000000
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
-0.197100 0.549500 0.850400 -0.689700 -2.819900
-4.393000 -5.111500 -5.205690 -4.654785
#phi = 0.000000
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
-3.450950 -3.620070 -3.412065 -2.349860
#phi = 15.000000
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
-2.819900 -0.689700 0.850400 0.549500 -0.197100
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
-1.560780 -1.452885 1.432450 -0.902080
#phi = 30.000000
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
-2.137600 -0.171000 0.599600 0.497200 0.054300
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
1.496470 0.430085 -1.631110 -3.675795
#phi = 45.000000
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
-1.820600 -0.491100 0.257500 0.441500 0.077000
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
-3.037100 -2.343900 -0.831300 0.568500 0.768200
-0.196160 -1.922530 -3.816620 -5.298400
#phi = 60.000000
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
-1.530700 -0.663000 0.039200 0.262600 -0.174700
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
-1.710200 -3.283200 -4.640100 -5.355100
#phi = 75.000000
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
-2.252200 -3.364700 -4.109000 -4.268200
#phi = 90.000000
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
-2.054300 -2.785300 -3.199500 -3.181100
#phi = 105.000000
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
0.494000 0.584300 0.553500 0.496000 0.107000
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
-0.918300 0.734000 0.144700 -0.429100 -0.980600
-1.577700 -2.135600 -2.473700 -2.487000
#phi = 120.000000
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
0.881800 1.133600 1.245300 1.098100 0.308700
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
0.976300 0.634600 0.321300 -0.015100 -0.401000
-0.896500 -1.447900 -1.860700 -1.965500
#phi = 135.000000
-1.208900 -0.823200 -0.315500 0.246000 0.765300
1.193900 1.521300 1.668300 1.322000 0.279600
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
0.670300 0.850100 0.879300 0.737600 0.454400
-0.112400 -0.817500 -1.319200 -1.429400
#phi = 150.000000
-0.533400 -0.209000 0.150600 0.562200 0.995600
1.435200 1.833100 1.984800 1.517000 0.407900
-0.934600 -2.036600 2.959500 0.738500 0.065700
0.615100 1.302200 1.618100 1.641000 1.168000
0.365300 -0.379800 -0.804600 -0.807400
#phi = 165.000000
0.019900 0.182800 0.348400 0.623800 1.027400
1.529800 2.026400 2.205800 1.713100 0.594100
-0.730100 3.704000 0.837800 -0.703500 -0.373700
0.688500 1.683900 2.188200 2.046200 1.392400
0.620800 0.014200 -0.269700 -0.203800

28
examples/charmm/1hvn/colvar.index Normal file
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@ -0,0 +1,28 @@
[ bb_rmsd ]
1 5 17 18 19 21 39 40 41 43
50 51 52 54 70 71 72 74 84 85
86 88 95 96 97 99 102 103 104 106
124 125 126 128 139 140 141 143 146 147
148 150 163 164 165 167 182 183 184 186
192 193 194 196 216 217 218 220 230 231
232 234 241 242 243 245 265 266 267 269
275 279 280 283 305 307 308 309 310 311
312 315 335 337 338 339 340 341 342 345
368 370 371 372 373 374 375 378 398 400
401 402 403 404 405 408 428 430
[ sc_rmsd ]
7 9 13 23 26 29 32 35 45 48
56 59 60 62 64 66 68 76 79 80
81 90 93 108 111 114 117 120 130 133
136 137 138 152 155 157 158 160 161 169
171 175 178 188 198 201 204 207 209 210
213 222 225 226 227 236 239 247 250 253
256 258 259 262 271 276 277 285 286 288
289 290 291 293 294 296 297 298 299 302
317 318 320 321 323 325 326 327 328 329
332 347 348 350 351 352 355 356 357 359
360 361 362 363 365 380 381 383 384 386
388 389 390 391 392 395 410 411 413 414
416 418 419 420 421 422 425

1
examples/charmm/1hvn/restraints/constraint_angletype Normal file
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@ -0,0 +1 @@
variable constraint_angletype string "142"

10247
examples/charmm/1hvn/restraints/posres.xyz Normal file
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File diff suppressed because it is too large Load Diff

40
examples/charmm/1hvn/restraints/step4.0_minimization.col Normal file
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@ -0,0 +1,40 @@
###Lipid Head###
Colvarstrajfrequency 100
Colvarsrestartfrequency 100
indexFile colvar.index
colvar {
name bb_rmsd
rmsd {
atoms {
indexGroup bb_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars bb_rmsd
centers 0
forceConstant 1.0
}
colvar {
name sc_rmsd
rmsd {
atoms {
indexGroup sc_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars sc_rmsd
centers 0
forceConstant 0.1
}

40
examples/charmm/1hvn/restraints/step4.1_equilibration.col Normal file
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@ -0,0 +1,40 @@
###Lipid Head###
Colvarstrajfrequency 100
Colvarsrestartfrequency 100
indexFile colvar.index
colvar {
name bb_rmsd
rmsd {
atoms {
indexGroup bb_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars bb_rmsd
centers 0
forceConstant 1.0
}
colvar {
name sc_rmsd
rmsd {
atoms {
indexGroup sc_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars sc_rmsd
centers 0
forceConstant 0.1
}

40
examples/charmm/1hvn/step3_input.col Normal file
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@ -0,0 +1,40 @@
###Lipid Head###
Colvarstrajfrequency 100
Colvarsrestartfrequency 100
indexFile colvar.index
colvar {
name bb_rmsd
rmsd {
atoms {
indexGroup bb_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars bb_rmsd
centers 0
forceConstant $bb
}
colvar {
name sc_rmsd
rmsd {
atoms {
indexGroup sc_rmsd
}
refPositionsFile restraints/posres.xyz
}
}
harmonic {
colvars sc_rmsd
centers 0
forceConstant $sc
}

25648
examples/charmm/1hvn/step3_input.data Normal file
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File diff suppressed because it is too large Load Diff

45
examples/charmm/1hvn/step4.0_minimization.inp Normal file
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@ -0,0 +1,45 @@
echo screen
variable dcdfreq index 50
variable outputname index step4.0_minimization
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 1
fix cmap all cmap charmmff.cmap
fix_modify cmap energy yes
read_data step3_input.data fix cmap crossterm CMAP
neighbor 2 bin
neigh_modify delay 5 every 1
velocity all create 303.15 73706 dist gaussian
include restraints/constraint_angletype
fix 1 all nvt temp 303.15 303.15 100.0
shell sed -e "s/\$bb/1.0/g" -e "s/\$sc/0.1/g" step3_input.col > restraints/${outputname}.col
fix restraint all colvars restraints/${outputname}.col output ${outputname}
thermo ${dcdfreq}
thermo_style custom step time xlo xhi ylo yhi zlo zhi etotal pe ke temp press ebond eangle edihed eimp evdwl ecoul elong temp vol
dump 1 all dcd ${dcdfreq} ${outputname}.dcd
dump_modify 1 unwrap yes
min_style cg
minimize 0.0 1.0e-8 10000 20000
write_dump all custom ${outputname}.dump id type x y z vx vy vz ix iy iz
write_data ${outputname}.data

50
examples/charmm/1hvn/step4.1_equilibration.inp Normal file
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@ -0,0 +1,50 @@
echo screen
variable dcdfreq index 2500
variable outputname index step4.1_equilibration
variable inputname index step4.0_minimization
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 1
fix cmap all cmap charmmff.cmap
fix_modify cmap energy yes
read_data step3_input.data fix cmap crossterm CMAP
variable laststep file ${inputname}.dump
next laststep
read_dump ${inputname}.dump ${laststep} x y z vx vy vz ix iy iz box yes replace yes format native
neighbor 2 bin
neigh_modify delay 5 every 1
include restraints/constraint_angletype
fix 1 all shake 1e-6 500 ${dcdfreq} m 1.008 a ${constraint_angletype}
fix 2 all nvt temp 303.15 303.15 100.0
shell sed -e "s/\$bb/1.0/g" -e "s/\$sc/0.1/g" step3_input.col > restraints/${outputname}.col
fix restraint all colvars restraints/${outputname}.col output ${outputname}
thermo ${dcdfreq}
thermo_style custom step time xlo xhi ylo yhi zlo zhi etotal pe ke temp press ebond eangle edihed eimp evdwl ecoul elong temp vol
dump 1 all dcd ${dcdfreq} ${outputname}.dcd
dump_modify 1 unwrap yes
reset_timestep 0
run 25000
write_dump all custom ${outputname}.dump id type x y z vx vy vz ix iy iz
write_data ${outputname}.data

46
examples/charmm/1hvn/step5_production.inp Normal file
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@ -0,0 +1,46 @@
echo screen
variable dcdfreq index 5000
variable outputname index step5_production
variable inputname index step4.1_equilibration
units real
boundary p p p
newton off
pair_style lj/charmmfsw/coul/long 10 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
special_bonds charmm
improper_style harmonic
timestep 2
fix cmap all cmap charmmff.cmap
fix_modify cmap energy yes
read_data step3_input.data fix cmap crossterm CMAP
variable laststep file ${inputname}.dump
next laststep
read_dump ${inputname}.dump ${laststep} x y z vx vy vz ix iy iz box yes replace yes format native
neighbor 2 bin
neigh_modify delay 5 every 1
include restraints/constraint_angletype
fix 1 all shake 1e-6 500 0 m 1.008 a ${constraint_angletype}
fix 2 all npt temp 303.15 303.15 100.0 iso 0.9869233 0.9869233 1000 couple xyz mtk no pchain 0
thermo ${dcdfreq}
thermo_style custom step time xlo xhi ylo yhi zlo zhi etotal pe ke temp press ebond eangle edihed eimp evdwl ecoul elong temp vol
dump 1 all dcd ${dcdfreq} ${outputname}.dcd
dump_modify 1 unwrap yes
dump 2 all custom ${dcdfreq} ${outputname}.dump id type x y z vx vy vz ix iy iz
dump_modify 2 append no
reset_timestep 0
run 50000
write_data ${outputname}.data