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An important function of CONGEN is the evaluation and manipulation of the potential energy of a macromolecular system. Two types of manipulation are supported. First, one can minimize the energy by adjusting the coordinates of all the atoms in order to reduce its value. Several minimization algorithms are provided. Second, one can solve Newton's equations of motion using the potential energy in order to obtain a dynamics trajectory.
The commands which invoke these three types of manipulation are all parsed by the same routine, and any common actions are done therein.
{ MINImize }
{ DYNAmics } repeat(keyword) repeat(keyword value)
{ ENERgy }
value ::= { real }
{ integer }
Syntactic ordering: All keywords and keyword value pairs can appear in any order.
Table of Keywords with references
Before the energy of a system can be evaluated and manipulated, a number of data structures must be present.
Second, a parameter set must be present. It must contain all parameters which are required by the PSF being used.
Third, coordinates must be defined for every atom in the system. An undefined coordinate has a particular value, and if two coordinates have the same value, division by zero will occur in the evaluation of the energy. If the positions of hydrogens are required, the hydrogen bond generation routine, see section HBUILD Command), must be called before the energy is evaluated. In the case of energy evaluations, CONGEN will ignore interactions involving undefined atom positions. However, minimization and dynamics will fail if any positions are unknown.
Fourth, provisions must be made for having a hydrogen bond list and a non-bonded interaction list. Having non-zero frequencies for updating this lists is one way, one can also read these lists in, see section READ -- Reads Data from External Sources, or generate them with separate commands, see section Generation of Hydrogen Bonds, or section Generation of Non-bonded Interactions.
All of these requirements can be met through the use of a restart file, see section Running Molecular Dynamics.
There exist several commands which can modify the way the potential energy is calculated or can affect the way energy manipulations are performed.
The CONSTRAINT command, see section Constraints, can be used to set constraints of various kinds. First, it can be used to set flags for particular atoms which will prevent them from being moved during minimization or dynamics. Second, it can be used to add positional constraint term to the potential energy. This term will be harmonic about some reference position. The user is free to set the force constant. Third, the user can place a harmonic constraint on the value of particular torsion angles in an attempt to force the geometry of a molecule. Fourth, atoms can be fixed in place. When atoms are fixed, they are not allowed to move at all. Any energy terms involving nothing but fixed atom are ignored, because they will have no effect. In addition the trajectories written by the dynamics command only have one copy of the fixed atom coordinates written. Thus, such trajectories take less disk space.
The SHAKE command, see section SHAKE -- Fixing Bond Lengths Or Angles in Dynamics, is used to set constraints on bond lengths and also bond angles during dynamics. It is very valuable in that it permits a larger step size to be used during dynamics. This is vital for dynamics where hydrogens are explicitly represented as the low mass and high force constant of bonds involving hydrogen require a ridiculously small step size.
The WEIGHT command, see section Set Weight Command Variables -- WEIGHT, is used to change the weights on each of the terms in the potential energy function. This is useful during dynamics with NMR constraints when one is interested in getting to the final solution as quick as possible.
The user interface commands, see section Interfacing to CONGEN, can be used to modify the calculation of the potential and to add another term to the potential energy.
The following table describes the keywords which apply to both minimization and dynamics. See section Generation of Non-bonded Interactions, for a more detailed description of the non-bonded options. See section Generation of Hydrogen Bonds, for more information on hydrogen bonds.
Keyword Default Purpose
NSTEP 100 The number of steps to be taken. For minimization, this
is the number of cycles of minimization, not the
number of energy evaluations. For dynamics, this is
the number of dynamics steps which is also equal to
the number of energy evaluations.
INBFRQ 50 The frequency of regenerating the non-bonded list.
The list is regenerated if the current step number
modulo INBFRQ is zero and if INBFRQ is non-zero.
Specifying zero prevents the non-bonded list from being
regenerated at all.
IHBFRQ 50 The frequency of regenerating the hydrogen bond list.
Analogous to INBFRQ.
non-bond- The specifications for generating the non-bonded list.
-spec
hbond- The specifications for generating the hydrogen bond list.
-spec
IPRINT 0 If given a non-zero value, causes the printing of
all contributions to the energy whose atoms are less
than IMAXP, more or less, every IPRINT cycles. Useful
in debugging although somewhat obsolete since the
analysis facility can provide the same information in
a more readable form. There may be bugs in the
frequency of when the printing occurs.
IMAXP 0 In conjunction with IPRINT, causes the print out of
contributions to the energy. This keyword determines
the largest atom number which has its contributions
printed. In some cases the check is made on all atoms
in the interaction; in others, the check is made on
just the first.
NPRINT 1 The frequency with which energies are printed during
course of dynamics or ABNR minimization.
The simplest minimization algorithm is steepest descents (SD). In each step of this iterative procedure, we adjust the coordinates in the negative direction of the gradient. It has one adjustable parameter, the step size, which determines how far to shift the coordinates at each step. The step size is adjusted depending on whether a step results in a lower energy. I.e., if the energy drops, we increase the step size by 20% to accelerate the convergence. If the energy rises, we overshot a minimum, so the step size is halved. Steepest descents does not converge in general, but it will rapidly improve a very poor conformation.
A second method is the conjugate gradient technique (CONJ)
which has better convergence characteristics (R. Flectcher & C.M.
Reeves, The Computer Journal 7:149 (1964)). The method is
iterative and makes use of the previous history of minimization steps as
well as the current gradient to determine the next step. It can be shown
that the method converges to the minimum energy in N steps for a
quadratic energy surface where N is the number of degrees of
freedom in the energy. Since several terms in the potential are
quadratic, it requires less evaluations of the energy and gradient to
achieve the same reduction in energy in comparison to steepest descents.
Its main drawback is that with very poor conformations, it is more
likely to generate numerical overflows than steepest descents. The
algorithm used in CONGEN has a slightly better interpolation scheme and
automatic step size selection.
A third method involves solving the Newton-Raphson minimization equations iteratively (NRAP). This procedure requires the computation of the derivative of the gradient which is a matrix of size O(n**2). The procedure here is to find a point where the gradient will be zero (hopefully a minimum in energy) assuming that the potential is quadratic. The Newton-Raphson equations can be solved by a number of means, but the method adopted for CONGEN involves diagonalizing the second derivative matrix and then finding the optimum step size along each eigenvector. When there are one or more negative eigenvalues, a blind application of the equations will find a saddle point in the potential. To overcome this problem, a single additional energy and gradient determination is performed along the eigenvector displacement for each small or negative eigenvalue. From this additional data, the energy function is approximated by a cubic potential and the step size that minimizes this function is adopted. The advantages of this method are that the geometry cannot remain at a saddle point, as sometimes occurs with the previous procedures, and that the procedure converges rapidly when the potential is nearly quadratic (or cubic). The major disadvantage is that this procedure can require excessive storage requirements, o(n**2), and computation time, o(n**3), for large molecules. Thus we are currently restricted to systems with about 200 atoms or less for this method. This method may not be used when Images are used (see section Symmetry and Molecular Images).
The fourth method available is an adopted basis Newton-Raphson method (ABNR) (D. J. States). This routine performs energy minimization using a Newton-Raphson algorithm applied to a subspace of the coordinate vector spanned by the displacement coordinates of the last (MINDIM) positions. The second derivative matrix is constructed numerically from the change in the gradient vectors, and is inverted by an eigen vector analysis allowing the routine to recognize and avoid saddle points in the energy surface. At each step the residual gradient vector is calculated and used to add a steepest descent step onto the Newton-Raphson step, incorporating the new direction into the basis set.
A fifth method involving an amalgam of conjugate gradient and steepest descents (GCSD) is currently unavailable due to a bug in the command parser.
In the table which follows, keywords enclosed in square brackets means that one can choose one in the set. Such enclosed keywords do not expect a value after them. All other keywords are used for specifying values, See section Syntax for Energy Manipulation Commands. The method column shows which method the keyword affects. See section Options Common to Minimization and Dynamics, for common variables.
Keyword Default Method Purpose
[ CONJ ] CONJ Do conjugate gradient minimization.
[ SD ] Do steepest descent minimization.
[ NRAP ] Do Newton-Raphson minimization.
[ ABNR ] [MASS] Do Adopted Basis Newton-Raphson minimization,
with mass weighted forces if specified.
[ CGSD ] This is to combine CONJ and SD (Not available)
STEP .02 ALL Initial step size for the minimization algorithms.
Reasonable values for the various methods are best
determined by trial and error.
PRTMIN 1 ALL A flag indicating how much to print during
minimization.
SD No effect
CONJ If less than 2, the energy is printed only once
each cycle. A setting of 2 shows the energy for
each evaluation plus variables used in the method.
NRAP if greater than 1, a brief overview of
the least squares cubic fitting procedure
given for eigenvalues less than TFREQ.
ABNR If less than 2, the energy is printed out only for
successful steps (improvements in total
energy). Some description of how the step was
chosen is printed if it is set to 2, and a
very verbose description is given for values
of 3 or higher.
NCGCYC 100 CONJ The number of conjugate gradient cycles executed
before the algorithm restarts. This number
will be automatically lowered to the shortest
hydrogen bond or non-bonded list update
frequency. The algorithm will fail if the
potential is changed will it is running.
PCUT .9999 CONJ If the cosine of the angle between the old and new
P vector is greater than PCUT, the algorithm will be
restarted. This prevents the algorithm from plodding
down the same path repeatedly. If PRTMIN is less
than 2, one effect of the restart is that the step
size will go its initial value. If this happens many
times, you've converged.
EIGRNG .0005 ABNR The smallest eigenvalue (relative to the largest)
that will be considered nonsingular.
MINDIM 5 ABNR The dimension of the basis set stored.
STPLIM 1.0 ABNR The maximum Newton Raphson step that will
be allowed.
STRICT 0.1 ABNR The strictness of descent. The energy of a new step
must be less than the previous best energy + STRICT
for the new step to be accepted.
MASS -- ABNR Use unweighted forces by default or mass weighted
if specified. Mass weights converge more slowly but
allow association with normal mode frequencies.
TFREQ 1.0 NRAP The smallest eigenvalue that is considered to be
non-negative (i.e. do cubic fitting on all
eigenvalues smaller than this).
NFREQ NATOM*3 NRAP The number of degrees of freedom to be
optimized (the number of lowest eigenvalues).
Use the default whenever practical.
TOLENR 0.0 ABNR A tolerance applied to the change in total energy
change during a cycle of minimization (NCYCLE steps)
If the energy change is less than or equal to
TOLENR, the minimization routine will exit.
TOLGRD 0.0 ABNR A tolerance applied to the average gradient during
a cycle of minimization. If the average gradient
is less than or equal to TOLGRD, the routine
will exit.
TOLITR 100 ABNR The maximum number of energy evaluations allowed
CONJ for a single step of minimization.
TOLSTP 0.0 ABNR A tolerance applied to the average step size during
a cycle of minimization. If the average step size
is less than or equal to TOLSTP, the routine
will exit.
In either algorithm, the choice of step size is very important. One must weigh the increased accuracy of using a small step size against the longer real time that can be simulated with a given amount of execution time when a larger step size is used. The time step may be entered in either picoseconds (using the TIMESTP keyword) or the internal AKMA units (using the AKMASTP keyword).
CONGEN provides information on the accuracy of the numerical solution. Since the system has no external forces, the total energy should be conserved. Numerical errors will result in some fluctuations in the total energy so a good test is to compare the fluctuations in total energy to the fluctuations in kinetic energy as these fluctuations are proportional to the heat capacity of the system. See the next node for a description of dynamics output.
Because the force constants for the bonds and bond angles are fairly large, it is reasonable under certain circumstances to constrain their values during dynamics. Such constraints are applicable if the harmonic motions are weakly coupled to other motions. The advantage of such constraints is that the step size of the numerical integration may be increased without sacrificing accuracy as these terms have the largest gradients in macromolecules simulated at physiological temperatures. We use the SHAKE algorithm for applying the constraints, see section SHAKE -- Fixing Bond Lengths Or Angles in Dynamics. SHAKE can be applied to just the bonds involved with hydrogens, all bonds, all bonds and the angles involving hydrogens, or all bonds and angles.
A dynamics run has basically four parts; initialization, heating, equilibration, and the simulation itself. Initialization means providing an initial position and velocity for all the atoms. Heating is the process of increasing the kinetic energy of the system up to a final temperature at which the simulation will be conducted. Equilibration is the process where the kinetic energy and the potential energy of the system evenly distribute themselves throughout the system. Only when the average temperature of the system stabilizes can one collect the trajectory information for analysis. The initial coordinates of a simulation are obtained after applying the minimization algorithm to a complete coordinate set. One cannot start with a system with a large potential energy as it will quickly heat up to unreasonable temperatures. For initializing the velocities, the user can specify zero velocity, a uniform distribution of kinetic energy along each coordinate with random sign of the motion along each axis (IASORS 0) or a Gaussian distribution of velocities (IASORS 1 the default). The temperature at which velocities are assigned is determined by FIRSTT and TSTRUC by the algorithm:
Tassign = 2*(FIRSTT-TSTRUC) + TSTRUC.
For a harmonic system equilibrated to TSTRUC equal partition of the energy will result in an equilibrated temperature of roughly FIRSTT. If TSTRUC is not specified 1.25*FIRSTT will be used for assignment.
The heating of a system is performed gently by increasing the kinetic energy by a small amount periodically. The number of integration steps between heating applications, the final temperature, and the kinetic energy increment are all user specified. In addition, there is a choice in the method of increasing the kinetic energy of the system. One may scale existing velocities or reassign them. The velocities can be scaled by either one scale factor calculated for the kinetic energy of the system averaged over many time steps or by scale factors established for each atom based on the ratio of its time averaged kinetic energy with that of the system. If reassignment is chosen, the velocities can have either a uniform or Gaussian distribution.
To equilibrate the structure, one can specify a window around the final temperature where velocity adjustments will be made. The choice of velocity adjustments is the same as described above for heating.
For the actual run, CONGEN will output the position and velocities of all atoms at intervals specified by the user. The temperature window can be set larger so that any gross conformational changes which result in a different potential energy will cause the temperature to be maintained.
At any time energy is added to the system, the angular momentum of the system will be reduced to zero and translational motion will be stopped. One can also request that these operations be performed at any time during the dynamics run.
When dynamics is used for simulated annealing, it is useful to use the TLIMIT option. This option applies a velocity damping to any atom whose temperature exceeds the limit. It is especially useful for solving structures using NMR constraints, see section NMR Constraints. Consider the case of two atoms which are supposed to be close in space, but are not at the beginning of the simulation. When they approach, they will both acquire substantial kinetic energy as they travel down the potential well. With the TLIMIT option, their velocity will be reduced so that they will not accelerate to such high speeds that the numerical integration of their motion will fail because the step size is too large. In addition, the velocity damping will help to hold them in position. You can see details of the damping process by turning on the TLIMIT debugging variable, see section Set Debugging Variables -- DEBUG.
The use of a restart file is essential for running dynamics. Since running dynamics requires storing various derivatives of the position with respect to time, this information must be stored for the life of the dynamics run. This capability is provided by the restart file. When the run is initiated, a restart file must be written using the IUNWRI keyword. As the dynamics routine complete NCYCLE steps of dynamics, the Fortran unit specified by IUNWRI will be rewound and a restart file will be written. In case of crashes, one has restart files corresponding to various points in the run. The CRASHU variable may prove valuable. Successive runs of CONGEN to continue the dynamics run must read the previous restart file using the IUNREA keyword and write it out for the next part of the run. See section Dynamics Output, for a description of these variables.
There are many numbers giving the frequency of actions to be taken during dynamics such as updating the non-bonded list, heating the molecule etc. Some of these numbers are adjusted along with the number of steps to run so that numbers all have a common divisor. At the present time, there are combinations which result in errors. At some point an attempt may be made to catalog all the actions, and check for erroneous processing. If one is interested in simulating the motion of part of the system with the rest of the system remaining fixed, it is possible to fix atoms in place. See section Fixing Atoms in Place, for more information. If this is done, there are several effect on the dynamics. First, since the system is now anchored in space, the center of mass motion and total angular velocity is never stopped. Second, the number of degrees of freedom used for calculating the temperature is set to the number of free atoms times 3 minus 6. Third, the coordinate and velocity trajectory files will contain the position of the fixed atoms only once, and all other records will hold just the moving atoms. This saves a great deal of disk space.
The trajectory produced by the dynamics procedure can be analyzed in great detail using the analysis facility (see section The Analysis Facility of CONGEN). In addition, trajectory files can be merged, broken in smaller pieces, and sampled at different intervals. See section Manipulating Trajectories, for details. Likewise, said operations can be performed on coordinate trajectories while rotating the coordinates to match a given coordinate set. See section Reorienting a Coordinate Trajectory, for details.
In the table of keywords which follow, one can select on keyword from a set of keywords enclosed in square brackets and such keywords take no values after them. All other keywords must be specified with a value (see section Syntax for Energy Manipulation Commands). See section Options Common to Minimization and Dynamics, for other variables which apply. See section The CONGEN System of Units: AKMA., for a description of the AKMA units system.
Keyword Default Purpose
[ VERL ] VERL Verlet algorithm is used for integration in dynamics.
[ GEAR ] Gear ( 6 vector ) algorithm is used for integration.
If SHAKE is used, GEAR option is overridden and Verlet
algorithm is used.
[ STRT ] STRT The dynamics is assumed to start from the input
[ ] coordinates using an assignment of velocities given by
[ ] IASVEL. No restart file is read.
[ REST ] The dynamics is restarted by reading the restart file
from unit IUNREA.
AKMASTP .02 Time step for Dynamics in AKMA units. The AKMASTP
TIMESTP keyword is used to enter a step size in AKMA units.
TIMESTP is used for picoseconds. The default value is
0.02 AKMA units (0.000977 picoseconds).
TOL 1.0E-6 Shake tolerance, i.e. the maximum relative error allowed
in the constraining of a SHAKEn bond length or bond angle.
IUNREA -1 Fortran unit from which the dynamics restart file should
be read. A value of -1 means don't read any file
IUNWRI -1 Fortran unit on which the dynamics restart file for
the present run is to be written. A value of -1 means
don't read any file.
IUNCRD -1 Fortran unit on which the coordinates of the dynamics run
are to be saved. A value of -1 means no coordinates should
be written. Unformatted output.
IUNVEL -1 Fortran unit on which the velocities of the dynamics run
are to be saved. -1 means don't write. Unformatted output.
KUNIT -1 Fortran unit on which the total energy and some of its
components along with the temperature during the run are
written using formatted output.
CRASHU -1 Fortran unit where a single DCL command file will be
written. If the machine crashes before a restart file
is written, this file won't be touched. If the crash
occurs after a restart is written but before the run
completes, this file will contain the line, "$ @CRASH".
If the run completes, the file will contain
the line, "$ @COMPLET". This allows for an automatic
recovery system after crashes.
NSAVC 5 The step frequency for writing coordinates.
NSAVV 5 The step frequency for writing velocities.
NPRINT 1 The step frequency for storing on KUNIT as well as printing
on unit 6, the total energy data of the dynamics run.
IPRFRQ 50 The step frequency for calculating averages and rms
fluctuations of the major energy values. If this
number is less than NTRFRQ and NTRFRQ is not equal to
0, square root of negative number errors will occur.
IHTFRQ 0 The step frequency for heating the molecule in increments
of TEMINC degrees in the heating portion of a dynamics
run. Zero means do no heating.
IEQFRQ 0 The step frequency for assigning or scaling velocities to
FINALT temperature during the equilibration stage of the
dynamics run.
NTRFRQ 0 The step frequency for stopping the rotation and translation
of the molecule during dynamics. This operation is done
automatically after any heating.
FIRSTT 0.0 The initial temperature at which the velocities have to be
assigned at to begin the dynamics run. Important only
for the initial stage of a dynamics run.
FINALT 298.0 The desired final ( equilibrium ) temperature
for the system. Important for all stages except initiation.
TEMINC 5.0 The temperature increment to be given to the system every
IHTFRQ steps. Important in the heating stage.
TSTRUC -999. The temperature at which the starting structure has been
equilibrated. Used to assign velocities so that equal
partition of energy will yield the correct equilibrated
temperature. -999. is a default which causes the
program to assign velocities at T=1.25*FIRSTT.
TWINDH 5.0 The temperature deviation from FINALT to be allowed on the
high temperature side.(+ve). i.e. high side of the
temperature window. Useful during equilibration.
TWINDL -5.0 The temperature deviation from FINALT to be allowed on the
low temperature side.(-ve). i.e. low side of the
temperature window. Useful during equilibration.
This number must specified as a negative number to
be meaningful.
TLIMIT 0.0 The temperature limit for atoms. When this option is
positive, CONGEN will compute the velocity that
corresponds to this temperature for all atoms. After
every dynamics time step, the new velocity for each
atom will be checked against this limit. If it is
exceeded, the atom's velocity will be lowered to the
limit, and a new corresponding position will be calculated.
The use of this option can result in a loss of energy
in the system. The limit should be set above the desired
temperature of the system, but CONGEN makes no check to
see that the limit is reasonable. Also, this option
only works with Verlet integration. It will also work
with the SHAKE algorithm.
IASORS 0 The option for scaling or assigning of velocities during
heating ( every IHTFRQ steps) or equilibration
(every IEQFRQ steps).
.eq. 0 - scale velocities.
.ne. 0 - assign velocities.
IASVEL 1 The option for different assignments of velocities.
.eq. 0 - zero velocity assignment
.gt. 0 - gaussian distribution of velocity. ( +ve )
.lt. 0 - uniform distribution of velocity. ( -ve )
kinetic energy of 3N velocity components are same.
ISEED 314159 The seed for the random number generator used for
assigning velocities.
ISCVEL 0 The option for two ways of scaling velocities.
.eq. 0 - single scale factor for all atoms
.ne. 0 - a scale factor for each atom proportional to the
kinetic energy average ratio between the system
and along every degree of freedom for that atom.
ICHECW 1 The option for checking to see if the average temperature
of the system lies within the allotted temperature window
(between FINALT+TWINDH and FINALT+TWINDL ) every
IEQFRQ steps.
.eq. 0 - do not check
i.e. assign or scale velocities.
.ne. 0 - check window
i.e. assign or scale velocities only if average
temperature lies outside the window.
ISCALE 0 This option is to allow the user to scale the velocities
by a factor SCALE at the beginning of a restart run.
This may be useful in changing the desired temperature.
.eq. 0 no scaling done ( usual input value )
.ne. 0 scale velocities by SCALE.
WARNING:
Please use this option only when you are changing the
temperature of the run.
SCALE 1.0 Scale factor for the previous option.
ETETEST 20.0 This variable is used for the total energy conservation
test in dynamics. If the total energy varies by more
than this amount and EKETEST multiplied by the kinetic
energy, the run will be terminated. This check is turned
off if TLIMIT is set.
EKETEST 0.1 See ETETEST above.
The first part of CONGEN's output after a dynamics command lists all of the options that apply to that part of the run. Then, any information about velocity assignments (temperature changes) follows. Any time the velocities are changed in an anisotropic way, the motion of and about the center of mass will be stopped. This results in a printout both before and after this operation of the `DETAILS ABOUT CENTRE OF MASS'. Its position and velocity are output followed by the components of the angular momentum. The last line gives the translation kinetic energy of the system, and thus one should expect a drop in the total energy and temperature of the system afterwards.
Non-bonded interaction and hydrogen bond updates will appear intermittently and are cleared labeled.
Every NPRINT steps, the total energy and various contributions will be printed. This output is preceded by a title which gives the correspondence of numbers to energy names. After IPRFRQ steps will appear the averages and RMS fluctuations. After the second such printout of averages and RMS fluctuations, the averages and RMS fluctuations for the run up to the last turning of the molecule will be given. This gives you longer range statistics. Such a calculation will not be done if IPRFRQ equals NTRFRQ. The ratio of total energy to kinetic energy fluctuations is an excellent measure of the accuracy of the run.
After the averages are printed, a least squares fit of the total energy against the step number will be made to look for drift in the energy. Two such values are printed, one for the last IPRFRQ steps, and one to the previous turn. Next, the initial energy for the statistics, both short range and long, are printed. Finally, the correlation coefficient of the energy versus step is given for both ranges. A value close to zero indicates no systematic drift; a magnitude near 1 means you have a real problem with the dynamics.
This process of printout continues until the end of the run is reached. Just before the last energy is printed will appear a message about the writing of coordinates and velocities to their respective files.
The trajectories produced from a dynamics calculation generally require some sort of additional processing to make them easier to analyze. Currently, two such commands are provided, MERGE and ROTATE. MERGE is described below, and ROTATE is described under the COMPARE command, see section Reorienting a Coordinate Trajectory.
Frequently, one generates a trajectory into small files to minimize the CPU time of one job. However, so many files are usually hard to manage so it is desirable to merge said files into larger units. This command provides that capacity. In addition, it is possible to break up the trajectory into smaller pieces and to sample the trajectory less frequently than originally generated.
MERGE DYN [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer]
[ VEL ] [OUTPUTU unit-number] [NFILE integer]
Option Default Purpose
[COOR] COOR Specification of the type of trajectory file. COOR is
[VEL ] coordinates; VEL is velocities.
FIRSTU 51 The first unit of the trajectory to be read.
NUNIT 1 The number of units to be read starting with FIRSTU
SKIP 1 Only those coordinate whose dynamics step number
modulo SKIP will be reoriented and written out.
OUTPUTU 61 The first unit number of the output trajectory
NFILE The number of coordinates written to each output file.
If left out, this will be set to the number of
coordinates in the first input file times the number of
input files. WARNING: This default will generate a bad
trajectory file if SKIP is not set to the interval
actually present in the trajectories. Further, if you
set its value to be larger than the number of
coordinates that are actually written in any output
file, you will have problems. The error that is
generated results from the control array in the
beginning specifying that there are more coordinates
than actually exist in the file. EOF errors will result
when the trajectory is read.
The title of the output trajectory will be copied from the input
trajectory.k
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