4.2 Calculation commands

There are the commands to perform 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.

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.

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.

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;

See also:
DIPOLE, MONITOR.

BELL   (UINT)Niter   (UINT)FirstAtom   (UINT)LastAtom
 

Iterative distance geometry optimizer using the Bellman - Ford - Fulkerson algorithm.

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.

Return message:
Minimization steps.

Example:
BFGS    100   1;

See also:
CNGDEL, GENETIC, POLYTOPE, RIGID, STEEP, TRUST.

CLONE   (UINT)CloneID
 

Copy the current coordinate set and the active atom flag to the memory.

Return message:
None.

Example:
CLONE    1;
CNGDEL    100   0   0.01;
RESTORE    1;

It clones the current coordinate set, performs an energy minimization and, finally, restores the coordinate set from the clone ID 1. In this way, the energy minimization is performed without changing the starting atomic coordinates.

See also:
RESTORE.

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.

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.

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.

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.

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.

Return message:
Optimization step.

Example:
None.

See also:
EXPAND, ORBIT.

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.

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.

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).

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.

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.

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.

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.

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.

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;

See also:
MOMADD, MOMPAR.

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.

Return message:
None.

Example:
MOMADD    1   100;

See also:
MOM, MOMPAR.

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.

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.

Return message:
None.

Example:
NZINACTIVE    20   78;

See also:
ACTIVE, INACTIVE.

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.

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.

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.

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.

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.

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.

RESTORE   (UINT)CloneID
 

Copy a coordinate set and the active atom flag from the memory.

Return message:
If the clone ID is not available, an error message is shown.

Example:
RESTORE   1;

See also:
CLONE.

RICHARD   (CHAR)Who   (UINT)Nstep   (FLOAT)MDparam1    (FLOAT)MDparam2    (FLOAT)MDparam3
 

Thermodynamic path integrals using the Feynmann Weiner Kac approach (Wiener version).

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.

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.

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   (UFLOAT)Base   (UINT)Steps   (UFLOAT)TorWin
 

Define a torsion for the conformational search.

Return message:
Error message if an illegal parameter is present.

Example:
TGROUP   1   7   12   13   14   0.0   6   30.0;

See also:
TJUMP, TRANDOM, TSEARCH.

TJUMP   (UINT)Niter   (UINT)MinIter   (UFLOAT)MinToler   (UFLOAT)Temp   (UFLOAT)Rmsd
 

Perform the Boltzmann jump conformational search rotating randomly the active torsions. The amplitude of the torsion changes is  defined by the torsion window values (see TGROUP command). Base value defined by TGROUP is ignored and so the random perturbation is done starting from the original conformation. The number of the torsions that can be used to generate the conformations is unlimited. At the end of the conformational search, the memory contains the best conformation found.
The Boltzmann jump method allows upward energy jumps: if the potential of the new random generated conformer is lower than the previous one, it will be selected as reference conformation, but if the potential is higher than the previous one, a stochastic decision is requested. The probability of selecting the new conformation is equal to the Boltzmann factor:

F = e^-ΔE/RT

where ΔE is the potential difference between the two conformers, R is the gas constant (1.987 cal · K^-1 · mol ^-1) and T is the temperature in Kelvin.  A random number N is generated in the range from 0 to 1 and if N > F, the conformation is selected, otherwise (N < F) the conformation is rejected. The chances of making an upward jump in energy are greater at a higher temperature (T) or at a smaller energy difference (E).
The starting conformation undergoes a thermal perturbation in which the selected torsion are randomly rotated and if the resulting conformation is of lower energy, that's selected. If the perturbed conformation is of higher energy, the stochastic decision is requested, as explained above, to select or reject the new conformation. The random perturbation is carried out until the root mean square deviation (RMSD) between the reference and the new conformation exceeds the specified maximum RMSD value. When this condition is reached, the conjugate gradients minimization is performed and the resulting conformation is selected as new reference.
If the Boltzmann jump parameters are wrong, it's possible that the condition to exit from the perturbation phase is never reached. To avoid this problem, the MxPerIter variable sets the maximum number of perturbation iteration over which the procedure is stopped and the generated conformation is minimized.

Return message:
AMMP shows the random search steps:

  Starting Boltzmann jump search (100 steps, 2000.0 K, 60.00 perturbation RMSD)

  Tjump      1: ps    1, vb 111.135, v 174.606, vmin 117.072
  Tjump      2: ps    5, vb 111.135, v 64992120832.000, vmin 115.894
  Tjump      3: ps    1, vb 111.135, v 4584.223, vmin 114.690
  Tjump      4: ps    1, vb 111.135, v 688399360.000, vmin 113.482
  Tjump      5: ps    8, vb 111.135, v 275.485, vmin 119.162
  Tjump      6: ps    1, vb 111.135, v 1170.165, vmin 126.796
  Tjump      7: ps    1, vb 111.135, v 1498841.500, vmin 122.223
  Tjump      8: ps    1, vb 111.135, v 34582256.000, vmin 121.838
  Tjump      9: ps    3, vb 111.135, v 161768.172, vmin 117.854
  Tjump     10: ps    1, vb 111.135, v 8072.150, vmin 116.928
  Tjump     11: ps    1, vb 111.135, v 573.954, vmin 125.318
  ...

  Best conformation selected (v 93.904305)

In each line is shown: the conformational search step, the number of conformations generated during the thermal perturbation phase (ps), the lowest potential found (vb), the potential (v), and the potential of the minimized conformer (vmin). This last value is not shown if the conformer minimization is not performed or disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates are available in memory) and it shows its potential (v).

Example:
TJUMP   3000   20   0.0   500;

See also:
TGROUP, TMIN, TRANDOM, TSEARCH.

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.

Return message:
None.

Example:
TMAP   7   12   13   14   12   13   14   15   20   20;

See also:
TJUMP, TMIN, TRANDOM, TSEARCH, TSET.

TMIN   (UINT)Atom1   (UINT)Atom2   (UINT)Atom3   (UINT)Atom4   (UINT)Steps
 

Minimize a torsion systematically rotating it.

Return message:
Show the torsion search steps and the final torsion value:

  Starting the torsion minimizer (angle 91.845, steps 24)

  Tmin       1: angle 15.000, v 41.004, vb 41.004
  Tmin      11: angle 165.000, v 28.959, vb 22.675
  Tmin      21: angle 315.000, v 24.826, vb 22.675
  Tmin      24: angle 360.000, v 34.080, vb 22.675

  Best conformation selected (angle 105.000, v 22.674868)

Example:
TMIN   7   12   13   14   24;

See also:
TGROUP, TJUMP, TMAP, TRANDOM, TSEARCH, TSET.

TPAC   (UINT)Nstep   (FLOAT)Dtime   (UFLOAT)Temp
 

Temperature constrained molecular dynamics.

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.

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, TJUMP, TMAP, TMIN, TRANDOM, 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.

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.

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.

TRANDOM   (UINT)Niter   (UINT)MinIter   (UFLOAT)MinToler   (BOOL)KeepPrev   (BOOL)KeepMin
 

Perform the random conformational search rotating randomly the active torsions. The torsion starting value and the torsion windows are set by the TGROUP command. The torsion window is The number of the torsions that can be used to generate the conformations is unlimited. At the end of the conformational search, the memory contains the best conformation found.

Return message:
AMMP shows the random search steps:

  Starting random conformational search (100 steps)

  Trandom    1: v 14123088896.000, vb 14123088896.000, vmin 113.733
  Trandom    2: v 18819.949, vb 113.733, vmin 107.588
  Trandom    3: v 307.890, vb 107.588, vmin 114.008
  Trandom    4: v 136.162, vb 107.588, vmin 112.244
  Trandom    5: v 17879676928.000, vb 107.588, vmin 118.615
  Trandom    6: v 18261741568.000, vb 107.588, vmin 127.483
  Trandom    7: v 161.983, vb 107.588, vmin 113.163
  Trandom    8: v 685030.000, vb 107.588, vmin 109.987
  Trandom    9: v 30623124.000, vb 107.588, vmin 1561.937
  Trandom   10: v 159.711, vb 107.588, vmin 108.041
  ...

  Best conformation selected (v 101.695412)

In each line is reported: the conformational search step, the potential (v), the best potential found at that step (vb) and the potential of the minimized conformer (vmin). This last value is not shown if the conformer minimization is disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates are available in memory) and it shows its potential (v).

Example:
TRANDOM   1000   20   0.0   0   0;

See also:
TGROUP, TMIN, TSEARCH.

TSEARCH   (UINT)MinIter   (UFLOAT)MinToler
 

Perform the systematic conformational search (grid scan) rotating  systematically the active torsions. The torsion starting value and the number of rotation steps are set by the TGROUP command. The number of the torsions that can be used to generate the conformations is unlimited. At the end of the conformational search, the memory contains the best conformation found.

Return message:
AMMP shows the torsion search steps:

  Starting systematic conformational search (6 steps)

  Tsearch    1: v 142.206, vb 142.206, vmin 107.684
  Tsearch    2: v 134.114, vb 107.684, vmin 108.797
  Tsearch    3: v 138.397, vb 107.684, vmin 107.635
  Tsearch    4: v 135.108, vb 107.635, vmin 111.325
  Tsearch    5: v 141.933, vb 107.635, vmin 110.274
  Tsearch    6: v 136.650, vb 107.635, vmin 106.573

  Best conformation selected (v 106.573456)

In each line is reported: the conformational search step, the potential (v), the best potential found at that step (vb) and the potential of the minimized conformer (vmin). This last value is not shown if the conformer minimization is disabled (see the MinIter parameter).
The last line informs that the best conformer found is selected (its coordinates are available in memory) and it shows its potential (v).

Example:
TSEARCH   20   0.0;

See also:
TGROUP, TMIN, TRANDOM.

USE   (CHAR)FFTerm   ...
 

Select the force field terms for energy calculation. By the same command, you can select more then one term.

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.

Return message:
None.

Example:
V_MAXWELL   300.0;

See also:
DOUBLETIME, HPAC, PACPAC, PAC, PPAC, PTPAC, RICHARD, TPAC, V_RESCALE, VERLET.

V_RESCALE   (UFLOAT)Temp
 

Rescale the velocities to a new temperature.

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.

Return message:
None.

Example:
VERLET   1000   0.00001;

See also:
DOUBLETIME, HPAC, PACPAC, PAC, PPAC, PTPAC, RICHARD, TPAC, V_MAXWELL, V_RESCALE.