4.2 Calculation commands
There are the commands to perform the AMMP calculations.
ABUILD (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
Analytic geometry solver. It use resultants to build atoms based on three or
more distances and the distance/planarity to build based on one or two
distances. The maximum number of atoms is 800.
Parameters: | ||
Niter | Number of iterations. If it's less then 1, one iteration only is performed. | |
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. |
Return message:
Build steps.
Example:
ABUILD 50 1 95;
See also:
BELL, DGEOM, GSDG,
KOHONEN.
ACTIVE
(UINT)FirstAtom (UINT)LastAtom
Activate the atoms for the next calculations. The inactive atoms aren't
considered and they are kept fixed.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
None.
Example:
ACTIVE 1 1200;
See also:
INACTIVE, NZINACTIVE.
ANALYZE
(UINT)FirstAtom (UINT)LastAtom
Evaluate the non-bond interaction energy, showing the complete non-bonded and
electrostatic energies for the specified atom range ( I-J ). This command is
useful for determining the interaction energy of a protein/substrate complex.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the FirstAtom only is considered. |
Return message:
AMMP shows the energy for each atom in the selection range:
Vnonbon internal lys.n 137 Eq -12.860423 E6 -1.397398 E12 2.191076 Vnonbon external lys.n 137 Eq 16.632879 E6 -5.806829 E12 9.177713 Vnonbon total lys.n 137 Eq 3.772456 E6 -7.204227 E12 11.368790
where internal is intramolecular energy, external is the intermolecular (interaction) energy, total is the sum of intramolecular and intermolecular energies, Eq is the electrostatic (coulombic) energy, E6 and E12 are the Lennard - Johnes terms. At the end of the atom dump, AMMP reports:
Vnonbon total internal 151.439880 Vnonbon total external 2.272158 Vnonbon total 153.712067 153.712067 non-bonded energy 153.712067 total potential energy
where Vnonbon total internal is the total intramolecular energy, Vnonbon total external is the total intermolecular (interaction) energy, Vnonbon total is the total non-bond interaction energy (it's the sum of Vnonbon total internal and Vnonbon total external). Non-bonded energy and total potential energy are self explaining.
Example:
ANALYZE 137 158
BELL (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
Iterative distance geometry optimizer using the Bellman - Ford - Fulkerson
algorithm.
Parameters: | ||
Niter | Number of iterations. If it's less then 1, one iteration only is performed. | |
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
Build steps.
Example:
BELL 20 1;
See also:
ABUILD, DGEOM, GSDG,
KOHONEN.
BFGS (UINT)Niter
(UFLOAT)Toler
BFGS Quasi-Newton
minimizer. If the available memory isn't enough, the minimization is
automatically switched to CNGDEL.
Parameters: | ||
Niter | Number of iterations. | |
Toler | Tolerance value. |
Return message:
Minimization steps.
Example:
BFGS 100 1;
See also:
CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
CNGDEL (UINT)Niter
(UINT)Nreset (UFLOAT)Toler
AMMP uses the
Poliak-Ribeire algorithm for conjugate gradients with an inexact line search.
AMMP will only terminate conjugate gradients when the number of steps is
exhausted, or the calculated gradients are not a descent direction.
Parameters: | ||
Niter | Number of iterations. | |
Nreset | Number of iterations resetting to steepest descent (STEEP). | |
Toler | It'st he desired value of the l_inifinity norm for the force. |
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force, and the value of b which is the conjugate dot product. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
The RMS force can be found by examining the value of the variable l2f (nop l2f;
or dump variable) which is the sum of the squares of the forces.
Example:
CNGDEL 100 0 0.01;
See also:
BFGS, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
DGEOM (UINT)Nstep
(UINT)Origin (FLOAT)Shift
Standard distance geometry optimizer implemented with the power method.
Parameters: | ||
Nstep | Number of steps. If it's less then 1, one iteration only is performed. | |
Origin | It's the atom serial used as the key atom. | |
Shift | Amount of eigenvalue shift. |
Return message:
Build steps.
Example:
DGEOM 20 1 0.5;
See also:
ABUILD, BELL, GSDG,
KOHONEN.
DIPOLE
(UINT)FirstAtom (UINT)LastAtom
Calculate the dipole
moment.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
Dipole moment:
Dipole warning, 1 10 sum charge is not zero -1.000002 Dipole 1 10 center of charge is 0.237469 -0.059340 -0.008954
Example:
DIPOLE 1;
See also:
MONITOR.
DOUBLETIME
(UINT)Nstep
(UFLOAT)Dlong (UFLOAT)Dshort (UFLOAT)Temper
Double the time scale in molecular dynamics, performing a non linear fit and
extrapolation.
Parameters: | ||
Nstep | Number of iterations. | |
Dlong | Time scale. | |
Dshort | Time step in m/s (0.00001 for 1 fs time integration). | |
Temper | Temperature in Kelvin (default 300K). |
Return message:
MD steps.
Example:
DOUBLETIME 1000 2 0.00001
300;
See also:
HPAC, PAC, PACPAC,
PPAC, PTPAC, RICHARD,
TPAC,
V_MAXWELL, V_RESCALE,
VERLET.
DSCF
(CHAR)What
(UINT)Niter (UFLOAT)Toler
Direct SCF orbital
optimizer.
Parameters: | ||||
What | It could be: ANA (report only), CHARGE, COEF (coefficients), EDMAP, EMPIR, EXPO (exponents), FRE (freeze), GAN (gang toghether), GEOM (orbital geometry), IGEOM, INDO, IPOLI, PHIMAP, POLI, THA (thaw), XYZ (atom center). | |||
Niter |
|
|||
Toler | Tolerance value. |
Return message:
Optimization step.
Example:
None
GDOCK (UFLOAT)Toler
(UINT)Ndeep (UINT)Niter (FLOAT)VarA
(FLOAT)VarX (UINT)FirstAtom
(UINT)LastAtom
Genetic algorithm rigid docking. The specified atom range is docked into the
rest of the structure.
Parameters: | ||
Toler | It'st he desired value of the l_inifinity norm for the force. | |
Ndeep | Number of possible solutions (population). In the initialization phase of the genetic algorithm the starting population is generated rototranslating randomly the selected atoms using the VarA and VarX scale factors. The default value is 8. | |
Niter | Number of iterations (default 1). | |
VarA | Rotation scale factor used to generate the starting population (default 1.0). | |
VarX | Translation scale factor used to generate the starting population (default 1.0). | |
FirstAtom | First atom number (not serial) of the selection (default 1). | |
LastAtom | Last atom number (not serial) of the selection (default last atom). |
Return message:
Calculation steps steps.
Example:
GDOCK 1 10 100 1.0 1.0 145;
See also:
None.
GENETIC (UINT)Niter
(UINT)Ndeep (FLOAT)Sigma
(FLOAT)Target (UINT)NoptSteps
Genetic algorithm
minimizer.
Parameters: | ||
Niter | Number of iterations. | |
Ndeep | Number of possible solutions (population). In the initialization phase of the genetic algorithm the start population is randomly generated using the starting coordinates adding a random number (from 0 to 1) multiplied by the Sigma scale factor. | |
Sigma | Scale factor used to generate the starting population. | |
Target | When the population satisfies the Target value, the minimization is stopped. | |
NoptSteps | Optimization steps with conjugate gradients method. (CNGDEL). |
Return message:
Minimization steps.
Example:
GENETIC 1000 10 1.0 0.01
10;
See also:
BFGS, CNGDEL,
POLYTOPE, RIGID, STEEP,
TRUST.
GRASP (UINT)Niter
(UINT)NoptSteps (UINT)FirstAtom
(UINT)LastAtom (CHAR)Atom
Torsion space optimizer. It searches a space of torsions using the current
potentials and greedy algorithms. At least four atoms are required in the
selection range (FirstAtom - LastAtom).
Parameters: | ||
Niter | Number of iterations. | |
NoptSteps | Optimization steps with conjugate gradients method. (CNGDEL). | |
FirstAtom | First atom number (not serial) for selection (optional, default = first atom). | |
LastAtom | Last atom number (not serial) for selection (optional, default = last atom). | |
Atom | Atom name in the atom selection (optional). |
Return message:
Minimization steps.
Example:
GRASP 100 10 1 100
c;
See also:
None.
GSDG (UINT)Niter
(UINT)FirstAtom (UINT)LastAtom
GSDG or Gauss-Siedel Distance Geometry is a hybrid Krylov solver for distance
geometry. It's related to the earlier Herman's minimizer used in programs like
FRODO and CHAIN, but is more robust and has a stronger theoretical background.
GSDG understands bond, angle, nonbon, and noel
potentials. It can work on any combination of these terms. It systematically,
one atom at a time, attempts to solve the distance equations. The non-bonded
exclusion target is set to 4.5 Ångstroms. This is too large and results in a
distorted structure when the non-bonded terms are used. However this distorted
structure is usually self-avoiding and readily corrected with conjugate
gradients (CNGDEL) to result in a structure with both good
geometry and self-avoidance.
GSDG is most useful for building simple small molecules, and adding moderate
sized chucks to a partial structure.
Only the number of cycles is required in which case all active atoms are
searched. If only one atom is specified then only it is searched. Otherwise the
range of atoms specified is searched. GSDG checks the atom range order and it
swap its terms if FirstAtom is greater than LastAtom.
Parameters: | ||
Niter | Number of iterations. If it's less then 1, one iteration only is performed. | |
FirstAtom | First atom serial for selection (optional, default = first atom). | |
LastAtom | Last atom serial for selection (optional, default = last atom). |
Return message:
Build steps.
Example:
GSDG 50;
See also:
ABUILD,
BELL, DGEOM.
HPAC (UINT)Nstep
(FLOAT)Dtime (FLOAT)Energy
Total energy constrained molecular dynamics, performing Nstep
PAC dynamics.
Parameters: | ||
Nstep | Number of steps. | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration). | |
Energy | Kinetic energy. |
Return message:
None.
Example:
HPAC 1000
0.00001 80.0;
See also:
DOUBLETIME, PAC, PACPAC,
PPAC, PTPAC, RICHARD,
TPAC,
V_MAXWELL, V_RESCALE,
VERLET.
INACTIVE
(UINT)FirstAtom (UINT)LastAtom
Inactivate the atoms for the next calculations. The inactive atoms aren't
considered and they are kept fixed.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
None.
Example:
INACTIVE 34 132;
See also:
ACTIVE, NZINACTIVE.
KOHONEN (UINT)Niter
(UFLOAT)Radius (INT)Initialize (UFLOAT)Rx (UFLOAT)Ry (UFLOAT)Rz
Kohonen neural network to find the 3D space filling curve corresponding to the
structure: the net links correspond to chemical bonds, angle distances, noel
distances and eventually the distance update could also include the Van der
Waals interactions and the chirality. The Kohonen algorithm implements a
self-organizing neural network that possess an isometry with self-assembling
physical systems. One particular system of interest is proteins and other
polymers.
Parameters: | ||
Niter | Number of iterations. | |
Radius | It's the sphere radius in Å used to initialize the starting coordinates (see Initialize). If it's a value less then 1.0 Å, it's automatically computed as square root of the number of atoms. | |
Initialize | If it's 1, the neural network is initialized assigning
random coordinates for each active atom. The inactive atoms, if they are
present, are used to calculate the geometry centre of the molecule. If no
inactive atoms are available, the geometry centre is placed at 0, 0, 0. The
random coordinates are scaled to Radius in order to fill completely
the sphere that will contain the final structure. If the Initialize value is -1, the neural network isn't initialized and it continues the previous calculation. |
|
Rx | Symmetry radii in Å:
The cylindrical and ellipsoidal symmetries ignore the Radius value, and the spherical symmetry uses the Radius value. |
|
Ry | ||
Rz |
Return message:
Build steps.
Example:
KOHONEN 100 -1 1
0.0
See also:
ABUILD,
BELL, DGEOM, GSDG.
MOM
(FLOAT)TotalCharge (UINT)Niter
Perform the MoM atomic charge calculation. The algorithm is based on the
moments developed by Rappe and Goddard. The atoms must be selected with the
MOMADD command before to start the MoM calculation.
Parameters: | ||
TotalCharge | Molecule total charge. | |
Niter | Number of iterations. If it's less then 0, the default number of iterations is performed (20). |
Return message:
Charge attribution steps with error value:
MoM : Initialization MoM 4: Error -1.440886e-01 MoM 8: Error -1.476538e-02
Example:
MOM -1.0 20
MOMADD
(UINT)FirstAtom (UINT)LastAtom
Select the atoms for the MoM calculation. It can be called
more then one time and the selection is lost when MOM is
executed.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
None.
Example:
MOMADD 1 100;
MONITOR
Perform a single point energy evaluation. The USE command allows to select the
energies to dump.
Parameters:
None
Return message:
Dump of energies in Kcal/mol:
Energy: Bond................: 1.080161 Angle...............: 2.006297 Torsion.............: 7.762559 Non-bond............: 10.683147 Hybrid..............: 1.009054 Total potential.....: 22.541220 Total kinetic.......: 0.000000 Total energy........: 22.541220 Total action........: -22.541220
Example:
MONITOR;
See also:
DIPOLE,
USE.
NORMAL
(UFLOAT)Damp
Calculate the normal modes. This is useful for small molecules.
Parameters: | ||
Damp | Normal scale factor. If it's equal to 0, the eigenvalues are dumped only. If it's greater then 0, the structures are dumped in PDB multi-model format. The resulting file (see output command) is readable by VEGA ZZ or by other molecular modelling softwares supporting the PDB multi-model format. |
Return message:
The computed Eigenvalues if Damp is less or equal to 0:
81 Eigenvalues found: 414.515198 kcal/A^2g 3126.659427 cm-1 412.284485 kcal/A^2g 3118.235021 cm-1 401.209595 kcal/A^2g 3076.068513 cm-1 400.785583 kcal/A^2g 3074.442639 cm-1 400.264404 kcal/A^2g 3072.442995 cm-1
Example:
NORMAL 0;
See also:
None.
NZINACTIVE
(UINT)FirstAtom (UINT)LastAtom
Inactivate the atoms which
aren't located at the axis origin (0, 0, 0). The inactive atoms aren't
considered and they are kept fixed.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. This is an optional argument. If it's omitted, the LastAtom is the last atom in the molecule. |
Return message:
None.
Example:
NZINACTIVE 20 78;
PAC (UINT)Nstep
(FLOAT)Dtime
Perform the molecular dynamics, predicting the path given current velocity,
integrating the force (Simpson's rule), predicting the final velocity and
updating the position using trapezoidal correction.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. |
Return message:
None.
Example:
PAC 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
PACPAC (UINT)Nstep
(FLOAT)Dtime
Perform the molecular dynamics, predicting the path given current velocity,
integrating the force (Simpson's rule), predicting the final velocity and
updating the position using trapezoidal correction. This is the more accurate
version of PAC.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration). The default value is 0.00001. |
Return message:
None.
Example:
PACPAC 1000
0.00001;
See also:
DOUBLETIME, HPAC, PAC,
PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
POLYTOPE
(UINT)FirstAtom (UINT)LastAtom (UINT)Niter
(UFLOAT)Vstart (UFLOAT)Vfinal
Perform a polytope simplex minimization on a selected range of atoms.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. If it's set to 0, the LastAtom is the last atom in the molecule. | |
Niter | Number of iterations. | |
Vstart | Starting variance. It's the scale factor used to move the atom coordinates. | |
Vfinal | Target (final) variance. |
Return message:
Minimization steps.
Example:
POLYTOPE 1 0 100
0.5 0.01;
See also:
BFGS, CNGDEL, GENETIC,
RIGID, STEEP, TRUST.
PPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Press
Pressure constrained molecular dynamics. The volumes are not fully calibrated in
this command. It is also necessary to slowly approach the desired conditions
because this uses Andersen's demon for volume constraints. Andersen's demon is
not fully stable and the system can explode.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. | |
Press | Pressure in kilopascal (101.325 kPa = 1.0 atm). |
Return message:
None.
Example:
PPAC 1000
0.00001 101.325;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PTAC,
RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
PTPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Temp
(UFLOAT)Press
Temperature and pressure constrained molecular dynamics. The volumes are not
fully calibrated in this command. It is also necessary to slowly approach the
desired conditions because this uses Andersen's demon for volume constraints.
Andersen's demon is not fully stable and the system can explode.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. | |
Temp | Temperature in Kelvin. | |
Press | Pressure in kilopascal (101.325 kPa = 1.0 atm). |
Return message:
None.
Example:
PTPAC 1000
0.00001 310 101.325;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
RICHARD, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
RICHARD
(CHAR)Who (UINT)Nstep
(FLOAT)MDparam1 (FLOAT)MDparam2 (FLOAT)MDparam3
Thermodynamic path
integrals using the Feynmann Weiner Kac approach (Wiener version).
Parameters: | ||
Who | Clculation type. It could be: PAC, PACPAC, TPAC, HPAC, PTPAC, VERLET. | |
Nstep | Number of steps (default 1). | |
MDparam1 | Optional parameters required by the specified calculation type. For more information, see the appropriate command section. | |
MDparam2 | ||
MDparam3 |
Return message:
None.
Example:
RICHARD PAC 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, TPAC, V_MAXWELL,
V_RESCALE, VERLET.
RIGID (UINT)FirstAtom
(UINT)LastAtom (UINT)Niter
(UFLOAT)Vstart (UFLOAT)Vfinal
Polytope rigid-body optimization.
Parameters: | ||
FirstAtom | First atom serial for selection. | |
LastAtom | Last atom serial for selection. If it's set to 0, the LastAtom is the last atom in the molecule. | |
Niter | Number of iterations. | |
Vstart | Starting variance. It's the scale factor used to move the atom coordinates. | |
Vfinal | Target (final) variance. |
Return message:
Optimization steps.
Example:
RIGID 1 0 100 0.5
0.01;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, STEEP,
TRUST.
STEEP (UINT)Niter
(UFLOAT)Toler
Steepest descent minimizer. If it's unable to satisfy the Toler value,
the minimization is automatically stopped.
Parameters: | ||
Niter | Number of iterations. | |
Toler | It's the desired value of the l_inifinity norm for the force. |
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
Example:
STEEP 100 1;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, TRUST.
TGROUP (UINT)Id
(UINT)Atom1 (UINT)Atom2
(UINT)Atom3 (UINT)Atom4
(FLOAT)Base (UINT)Steps
Define a torsion for
searching the torsion space.
Parameters: | ||
Id | Torsion identification number. It must be greater then 0. | |
Atom1 | Atom serials defining the torsion. | |
Atom2 | ||
Atom3 | ||
Atom4 | ||
Base | Starting torsion value in degree (default 0°). | |
Steps | Number of search steps (default 6). |
Return message:
None.
Example:
TGROUP 1
7 12 13 14 0 6;
See also:
TMAP, TMIN, TSEARCH,
TSET.
TMAP
(UINT)I1
(UINT)I2 (UINT)I3
(UINT)I4
(UINT)J1
(UINT)J2 (UINT)J3
(UINT)J4
(UINT)Isteps (UINT)Jsteps
Map two torsions rotating them systematically. It requires at least five atoms.
Parameters: | ||
I1 | Atom serials defining the first torsion. | |
I2 | ||
I3 | ||
I4 | ||
J1 | Atom serials defining the second torsion. | |
J2 | ||
J3 | ||
J4 | ||
Isteps | .Number of search steps for the first torsion (default 12). | |
Jsteps | Number of search steps for the second torsion (default 12). |
Return message:
None.
Example:
TMAP 7
12 13 14 12 13 14
15 20 20;
See also:
TGROUP, TMIN,
TSEARCH, TSET.
TMIN
(UINT)Atom1
(UINT)Atom2 (UINT)Atom3
(UINT)Atom4 (UINT)Steps
Search the torsion angle.
Parameters: | ||
Atom1 | Atom serials defining the torsion. | |
Atom2 | ||
Atom3 | ||
Atom4 | ||
Steps | Number of search steps (default 12). |
Return message:
Show the torsion search steps and the final torsion value:
Tmin 0: E 41.003773, Emax 41.003773 Tmin 4: E 23.803759, Emax 23.803759 Tmin 8: E 27.749823, Emax 22.674862 Tmin 12: E 41.699902, Emax 22.674862 Tmin 16: E 24.431847, Emax 22.674862 Tmin 19: E 33.479034, Emax 22.674862 Tmin : Original 91.845497, final 90.000000
Example:
TMIN 7
12 13 14 20;
See also:
TGROUP, TMAP,
TSEARCH, TSET.
TPAC (UINT)Nstep
(FLOAT)Dtime (UFLOAT)Temp
Temperature constrained molecular dynamics.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. | |
Temp | Temperature in Kelvin. |
Return message:
None.
Example:
TPAC 1000
0.00001 300;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, V_MAXWELL,
V_RESCALE, VERLET.
TSET
(UINT)Atom1
(UINT)Atom2 (UINT)Atom3
(UINT)Atom4 (FLOAT)TorVal
Set the torsion angle.
Parameters: | ||
Atom1 | Atom serials defining the torsion. | |
Atom2 | ||
Atom3 | ||
Atom4 | ||
TorVal | New torsion value in degree. |
Return message:
The new torsion value:
Tset : Original 91.845497, delta 88.154503, final -180.000000
Example:
TSET 7
12 13 14 180.0;
See also:
TGROUP, TMAP, TMIN,
TSEARCH.
TRUNC (UINT)Niter
(UFLOAT)Dtoler (UFLOAT)Toler
Truncated Newton method
minimizer. It's based on the idea that an exact solution of the Newton
equation at every step is unnecessary and can be computationally wasteful in the
framework of a basic descent method. Any descent direction will suffice when the
objective function is not well approximated by a convex quadratic and, as a
solution to the minimization problem is approached, more effort in solution of
the Newton equation may be warranted. Their appeal to scientific applications is
their ability to exploit function structure to accelerate convergence.
Parameters: | ||
Niter | Number of iterations. | |
Dtoler | Approximation to truncate the Newton equation. The default value is 0.001 and values less then 0.001 aren't allowed, resetting automatically to the default. | |
Toler | It's the desired value of the l_inifinity norm for the force. |
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force, and the value of b which is the conjugate dot product. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
The RMS force can be found by examining the value of the variable l2f (nop l2f;
or dump variable) which is the sum of the squares of the forces.
Example:
TRUST 3000 0.001 0.01;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
TRUST (UINT)Niter
(UFLOAT)Dtoler (UFLOAT)Toler
Trust-region based minimizer. If it's unable to satisfy the Toler value,
the minimization is automatically stopped. The theory is to move in a steepest
descent direction until the disagreement between observed and calculated
energies is too high.
Parameters: | ||
Niter | Number of iterations. | |
Dtoler | Disagreement value between observed and calculated energies. The default value is 0.1 and values less then 0.001 aren't allowed, resetting automatically to the default. | |
Toler | It's the desired value of the l_inifinity norm for the force. |
Return message:
During the iterations, AMMP prints the current potential, the l_inifinity norm
on the force. The
value for l_infinity will hop around as it is the magnitude of the maximum force
on any atom which can both increase and decrease.
Example:
TRUST 1000 0.1 1.0;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP.
TSEARCH (UINT)Tgrp1
(UINT)Tgrp2 (UINT)Tgrp3 (UINT)Tgrp4
(UINT)Tgrp5 (UINT)Tgrp6 (UINT)Tgrp7
(UINT)Tgrp8
Perform the torsion search using the previous defined torsions.
Parameters: | ||
Tgrp1 | Torsion group identification number. The maximum number of torsions is eight for each torsion search. The torsions must be defined by the TGROUP command. | |
Tgrp2 | ||
Tgrp3 | ||
Tgrp4 | ||
Tgrp5 | ||
Tgrp6 | ||
Tgrp7 | ||
Tgrp8 |
Return message:
None.
Example:
TSEARCH 1
2;
See also:
TGROUP, TMAP, TMIN,
TSET.
USE
(CHAR)FFTerm
...
Select the force field terms for energy calculation. Using the same command you
can select more then one term.
Parameters: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FFTerm |
Force field term. It could be:
|
Return message:
None.
Example:
USE none
bond angle torsion;
See also:
BFGS, CNGDEL, GENETIC,
POLYTOPE, RIGID, STEEP,
TRUST.
V_MAXWELL
(UFLOAT)Temp
(FLOAT)Dx (FLOAT)Dy
(FLOAT)Dz
Set the velocity
distribution with a random Maxwell - Boltzmann distribution.
Parameters: | ||
Temp | Temperature in Kelvin. | |
Dx | Starting velocity along the X axis (optional value, default 0). | |
Dy | Starting velocity along the Y axis (optional value, default 0). | |
Dz | Starting velocity along the Z axis (optional value, default 0). |
Return message:
None.
Example:
V_MAXWELL
300;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_RESCALE,
VERLET.
V_RESCALE
(UFLOAT)Temp
Rescale the velocities to a
new temperature.
Parameters: | ||
Temp | Temperature in Kelvin. |
Return message:
None.
Example:
V_RESCALE
300;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
VERLET.
VERLET
(UINT)Nstep
(UFLOAT)Dtime
Perform the leapfrogging
molecular dynamics. This is here for historical reasons and is
occasionally useful.
Parameters: | ||
Nstep | Number of steps (default 1). | |
Dtime | Time step in m/s (0.00001 for 1 fs time integration).The default value is 0.00001. |
Return message:
None.
Example:
VERLET 1000
0.00001;
See also:
DOUBLETIME, HPAC,
PACPAC, PAC, PPAC,
PTPAC, RICHARD, TPAC, V_MAXWELL,
V_RESCALE.