Dynamics: Description and Discussion There are three separate dynamics integrators available in CHARMM: Name Keyword Module Original Verlet ORIG dynamcv.src (default) Leapfrog Verlet LEAP dynamc.src (default with NIH compile flag) Velocity Verlet VVER dynamvv.src 4-D L-F Verlet VER4 dynam4.src All methods are based on the Verlet scheme, and when used without any special features, provide identical trajectories for short simulations. All methods allow SHAKE. The ORIG integrator is a standard 3-step Verlet integrator with few frills. It allows: Langevin Dynamics (LANG) Thermodynamic Simulation Method (TSM) The LEAP integrator is similar to the ORIG integrator, but does provide increased accuracy (esp. for single precision version of CHARMM). It allows: Langevin dynamics (LANG) (with accurate temperatures printed) Constant Temperature and Pressure (CPT) (based on Berendsen's method) Accurate pressures with SHAKE High frequency correction to the total energy Parallel code Free energy equilibration indicator (deltaF*V) (with PERT) Thermodynamic Simulation Method (TSM) The VVER integrator also provides increase accuracy. It allows: Constant Temperature (NOSE) (Nose-Hoover method) Multiple Time Step (MTS) The VER4 integrator enables the energy embedding technique that entails placing a molecule into a higher spatial dimension [Crippen, G. M. & Havel,T.F. (1990) J.Chem.Inf.Comput.Sci. Vol 30, 222-227]. The possibility of surmounting energy barriers with these added degrees of freedom may lead to lower energy minima. Here, this is accomplished by molecular dynamics in four dimensions. Specifically, another cartesian coordinates was added to the usual X, Y, and Z coordinates in the LEAPfrog VERLet algorithm. In order to generate a dynamics trajectory, all requirements for evaluating the energy must be met. See *note Energy:(energy.doc)Needs. * Menu: * Syntax:: Syntax of the dynamics command * Description:: Description of the keywords and options * Recommended:: Recommended input options and values * Discussion:: Running dynamics * Output:: Output from a dynamics run * Trajectory:: Trajectory manipulation and I/O * Merge:: Merging or breaking up trajectory files into different size pieces. Resampling at a larger interval. Least squares fit to a reference. * Reorient:: Reorienting a coordinate trajectory * RMSDyn:: Computes the RMS difference between two trajectories * Format:: formatting and unformatting a dynamics trajectory * Monitor:(monitor.doc). Monitor dihedral transitions * CPT dynamics:(pressure.doc). CPT dynamics * 4-D dynamics:(fourd.doc). 4-D dynamics * Pressure:(pressure.doc)Pressure. The pressure command * MTS:(mts.doc). Multiple Time Scales Method * Nose:(nose.doc). Nose-Hoover Dynamics

Syntax for the Dynamics Command DYNAmics {[LEAPfrog]} {[VERLet]} {STRT } {[TIMEstp real]} [NSTEp integer] - { ORIG } {LANGevin} {STARt } { AKMA real } { CPT } {VVER } {RESTart} { LEAPfrog } {VER4 } {[FIL4dimension]} {[SKBOnd]} {[SKANgle]} {[SKDIhedral]} {[SKVDerWaals]} {[SKELectrostatics]} nonbond-spec hbond-spec frequency-spec - unit-spec temperature-spec options-spec - cpt-spec four-dimension-spec hbond-spec::= see *note Hbonds:(hbonds.doc). nonbond-spec::= See *note Nbonds:(nbonds.doc). frequency-spec::= [INBFrq integer] [IEQFrq integer] [IHBFrq integer] [IHTFrq integer] [IPRFrq integer] [NPRInt integer] [NSAVC integer] [NSAVV integer] [NTRFrq integer] [ILBFrq integer] [ISVFRQ integer] unit-spec::= [IUNCrd integer] [IUNRea integer] [IUNVel integer] [IUNWri integer] [KUNIt integer] [CRAShu integer] [BACKup integer] temperature-spec::= [FINAlt real] [FIRStt real] [TEMInc real] [TSTRuc real] [TWINDH real] [TWINDL real] [TBATh real] options-spec::= [IASOrs integer] [IASVel integer] [ICHEcw integer] [ISCAle integer] [ISCVel integer] [ISEEd integer] [SCALe real] [NDEGg integer] [RBUFfer real] [AVERage] [ECHEck real] [TOL real] cpt-spec::= [ PCONst {[PINTernal]} [COMPressibility real] ] { PEXTernal } [PCOUpling real] [PREFerence real] [VOLUme real] [ TCONst [TCOUpling real] [TREFerence real] ] four-dimension-spec::= [K4DInitial real] [INC4Dforce integer] [DEC4Dforce integer] [MULTK4di real] [E4FILLcoordinates real]

Options common to minimization and dynamics The following table describes the keywords which apply to both minimization and dynamics. Keyword Default Purpose NSTEP 100 The number of steps to be taken. 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. INBFRQ = -1 --> all lists are updated when necessary (heuristic test). IHBFRQ 50 The frequency of regenerating the hydrogen bond list. Analogous to INBFRQ ILBFRQ 50 The frequency for checking whether an atom is in the Langevin region, defined by RBUF, or not. non-bond- The specifications for generating the non-bonded list. -spec See *note Nbonds:(nbonds.doc). hbond- The specifications for generating the hydrogen bond list. -spec See *note Hbonds:(hbonds.doc). [ 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. TIMESTP 0.001 Time step for dynamics in picoseconds. The default value is 0.001 picoseconds. 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. Formatted output. 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 10 The step frequency for writing coordinates. NSAVV 10 The step frequency for writing velocities. NPRINT 10 The step frequency for storing on KUNIT as well as printing on unit 6, the energy data of the dynamics run. IPRFRQ 100 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. ISVFRQ NSTEP The step frequency for writing a restart file. 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 300.0 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 10.0 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 -10.0 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. TBATH FINALT The temperature of the heatbath in Langevin dynamics. When set to zero it allows one to do purely dissipative (quenched) dynamics. RBUF 0.0 Inner radius of the buffer, or Langevin, region sphere. All atoms with radial positions greater than RBUF angstroms are propagated by Langevin dynamics, if the dynamics keyword LANGevin has been specified. IASORS 0 The option for scaling or assigning of velocities during heating (every IHTFRQ steps) or equilibration (every IEQFRQ steps). This keyword does not control the initial assignment of velocities. .eq. 0 - scale velocities. (use ISCVEL option) .ne. 0 - assign velocities. (use IASVEL option) IASVEL 1 The option for the choice of method for the assignment of velocities during heating and equilibration when IASORS is nonzero. This option also controls the initial assignment of velocities (when not RESTart) regardless of the IASORS value. .eq. 0 - Use the comparison coordinate values in AKMA units (sorry) with the STRT option. If NTRFRQ is positive, then net trans/rot will be removed first. This option supresses other assignments of velocity. .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. Scale factor for the previous option. NDEGF computed Number of degrees of freedom to use in computing the temperature. If not specified on any call, the value is computed. This specification is not remembered between successive calls to dynamics. AVERAGE no When saving coordinates every NSAVC steps, this option will cause the average structure of the last NSAVC dynamics steps to be written instead of the final snapshot coordinate set. This option is primarily used for making smooth movies. ECHECK 20.0 The maximum amount the total energy may change on any step. TOL 1.0E-10 The shake tolerance (if SHAKE is in use). PCONst false Flag to indicate that constant pressure code will be used. PINTernal true Flag to indicate that the internal pressure will be coupled the reference pressure. PEXTernal false Flag to indicate that the external pressure will be coupled to the reference pressure. PCOUpling 0.0 The coupling decay time in picoseconds for the pressure. A good value for this is 5 ps. COMPress 0.0 The compressibility in atm**-1. A good value for proteins is 4.63e-5 PREFerence 1.0 The reference pressure in atmospheres. VOLUme computed The volume in Angstroms**3 to use for the pressure calculation denominator. This value is calculated if the CRYStal feature is use. TCONst false Flag to indicate that constant temperature code will be used. TCOUpling 0.0 The coupling decay time in picoseconds for the temperature. A good value for this is 5 ps. TREFerence FINALT The reference temperature for constant temperature simulations.

Recommended CHARMM input for dynamics. This section is intended only as a guide in setting up a dynamics simulation input file. Changes should be made as necessary according to personal tastes and project requirements. 1) For heating and early equilibration: DYNAMICS LEAP VERLET RESTART(*) NSTEP 20000 TIMESTEP 0.001(+) - IPRFRQ 1000 IHTFRQ 1000 IEQFRQ 5000 NTRFRQ 5000 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 INBFRQ 25 - hbond-spec nonbond-spec - FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 - IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 10.0 TWINDL -10.0 (*) Except for first run, the use STRT in place of RESTART (+) If bonds to hydrogen atoms are SHAKEd 2) For late equilibration and analysis runs: DYNAMICS LEAP VERLET RESTART NSTEP 20000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 2000 IEQFRQ 5000(*) NTRFRQ 5000 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 - hbond-spec nonbond-spec - FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 - IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 1 TWINDH 10.0 TWINDL -10.0 (*) Window checking should be disabled for the analysis run (i.e. IEQFRQ=0) if you want a real microcanonical ensemble. 3) For heating, equilibration and analysis runs using Langevin dynamics:(+) DYNA LEAP LANGEVIN STRT(*) NSTEP 20000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 - ILBFRQ 1000 RBUFFER 0.0 TBATH 300.0 - hbond-spec nonbond-spec - FIRSTT 300.0 FINALT 300.0 - IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0 (+) Note that the friction coefficients, in units of 1/ps, must first be initialized by filling the array FBETA with the SCALAR command SCALAR FBETA SET <real> <optional atom selection> (*) Except for first run, the use STRT in place of RESTART 4) For quenched molecular dynamics: For the first run (STRT), read velocities into the comparison coordinate set, or this should directly follow a former dynamics command. DYNA VERLET STRT(*) NSTEP 10000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 200 IEQFRQ 200 NTRFRQ 400 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 - hbond-spec nonbond-spec - TSTRUC 300.0 FIRSTT 300.0 FINALT 0.0 TEMINC -30.0 - IASORS 0 IASVEL 0 ISCVEL 0 ICHECW 1 TWINDH 0.0 or equivalently with Langevin (dissipative) dynamics DYNA LANGEVIN STRT(*) NSTEP 10000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 4000 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 - hbond-spec nonbond-spec - TSTRUC 300.0 FIRSTT 300.0 FINALT 300.0 - ILBFRQ 1000 RBUFFER 0.0 TBATH 0.0 - IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 (*) For first run, use RESTART otherwise The IASVEL 0 option causes the comparison coordinates to be used for the initial velocities (AKMA units). For subsequent runs the options IASORS 1 and IASVEL 1 may be used if random velocities are to be periodically assigned. 5) For constant temperature and/or pressure dynamics DYNA LEAP VERLET STRT(*) NSTEP 20000 TIMESTEP 0.001 - IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 - IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 - NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 - PCONst PINTernal COMPress 4.63e-5 PCOUpling 5.0 PREFerence 1.0 - TCONst TCOUpling 5.0 TREFerence 300.0 - hbond-spec nonbond-spec - FIRSTT 300.0 FINALT 300.0 - IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

Running Molecular Dynamics The theoretical basis for dynamical simulations is elementary physics. The force on a particle is equal to the negative gradient of the potential energy of the particle. CHARMM can solve this equation numerically for all atoms in the molecule. A simple second order predictor two step method due to Verlet is used for integration. The choice of the integration 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 picoseconds (using the TIMESTP keyword). CHARMM 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 *note shake:(cons.doc)SHAKE. 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 velocities from the comparison coordinates (IASVEL 0), a uniform distribution of kinetic energy along each coordinate with random sign of the motion along each axis (IASVEL -1) or a Gaussian distribution of velocities (IASVEL 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. Velocities may also be passed to dynamics in the comparison coordinate set (as opposed to assignment). This allows the user considerable flexibility in setting up the initial conditions. The heating of 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 base ed 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, CHARMM 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. The use of a restart file is essential for running dynamics. The restart file contains information about the most recent coordinate sets necessary for the VERLET algorithm. In addition the values of the energy accumulators are stored. All other information (such as SHAKE, fixed atoms, harmonic constraints, friction coefficients) has to be regenerated before invoking a dynamics restart. When the run is initiated, a restart file must be written using the IUNWRI keyword. As the dynamics routine complete NCYCLE, see *note Output::, 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 CHARMM 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. Restarts may be done to reset various options, or to break up a long run into several shorter runs. Restart files will only run with the version of CHARMM they are created with. 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 *note fix:(cons.doc)fixed atom. 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. Trajectory files can be merged, broken in smaller pieces, and sampled at different intervals. Likewise, said operations can be performed on coordinate trajectories while rotating the coordinates to match a given coordinate set. When the DYNAmics command exits, the main coordinate set contains the final coordinate positions from the last energy evaluation and the comparison coordinates will contain the final velocities In AKMA units. Finally, a brief discussion of the Langevin dynamics algorithm is presented. The Langevin dynamics algorithm presently in CHARMM was intented to be used primarily with the "Stochastic Boundary Molecular Dynamics" method and consequently has been restricted to an algorithm which is valid only for the case FBETA*TIMESTEP<<1.0. That is for cases where relatively small friction coefficients are used. Typically values of FBETA*TIMESTEP up to about 0.3 still produce a stable dynamics which also satisfy the fluctuation-dissipation theorem. The algorithm itself reduces to the Verlet algorithm when FBETA is zero and consequently may be used to do regular dynamics, actually it is the same routine which does both dynamics. In using Langevin dynamics care must be taken to first initialize the array FBETA by using the scalar commands e.g., CHARMM >SCALAR FBETA SET <real> <atom selection> Failure to do this just means you are doing regular dynamics so no warning is given by CHARMM.

Contents of a dynamics output Note: This description of the output of a command is not normally going to be part of the documentation of commands. The dynamics output is sufficiently confusing that this description is necessary. The first part of CHARMM'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 upto 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.

Reading and writing trajectory frames with direct commands This facility allows the creation or manipulation of trajectory files The main uses of this facility are; 1) creating artificial trajectory files from coordinate frames 2) reading an existing trajectory frame by frame for analysis that requires access to a variety of CHARMM commands 3) modifying an existing trajectory (copy with changes) such as minimizing each frame or other operations. [Syntax TRAJectory command] =================================================================== There are three commands that comprise this facility. 1) Initializing trajectory I/O TRAJectory {read-spec} {write-spec} read-spec:== [IREAd unit] [NREAd int] [SKIP int] [BEGIN INT] [STOP INT] write-spec:== [IWRIte unit] [NWRIte int] [NFILE int] [EXPAnd] [NOTHer int] [DELTa real] [SKIP int] IREAd - first unit to read from (default: do not read) NREAd - number of units to read from (default:1) SKIP - skip value for both reading and writing (default:1) IWRIte - first unit to write to (default: do not write) NWRIte - number of units to write to (default:1) NFILe - number of frames on each output file (default: total) EXPAnd - flag to free fixed atoms in copying (only if reading) NOTHer - number of frames in previous files (if not reading) (d:0) DELTa - output delta value (if not reading) (default:0.001) 2) Reading a frame TRAJectory READ [COMP] 3) Writing a frame TRAJectory WRITe [COMP] The reading and writing commands do not have any specifiers other than whether the comparison or main coordinates will be used. =================================================================== There are three modes of operation; 1) Create a new trajectory. The IWRIte and NFILe keywords must be used. The default values for the others are listed above. If several files will be made in different CHARMM runs that will be linked together later, the NOTHer keyword value should be increased by NFILe on each subsequent run. EXAMPLE: Create a "movie" trajectory that involves the rotation of a single sidechain (residue 21). COOR AXIS SELE ATOM * 21 CA END SELE ATOM * 21 CB OPEN WRITE UNIT 22 FILE NAME TYR21.ROT TRAJECTORY IWRITE 22 NWRITE 1 NFILE 360 SKIP 1 * trajectory showing the rotation of sidechain 21 * SET 1 1 LABEL LOOP COOR ROTATE AXIS PHI 1.0 SELE ATOM * 21 * .AND. .NOT. ( TYPE C - .OR. TYPE N .OR. TYPE H ) END TRAJ WRITE INCR 1 BY 1 IF 1 LT 360.5 GOTO LOOP STOP =================================================================== 2) Reading an existing trajectory The IREAD keyword must be used. The default NFILe value is 1 and the remaining values if not specified will be read from the trajectory file. EXAMPLE: find the structure with the lowest energy and save it. UPDATE ... OPEN READ UNIT 22 FILE NAME DYN1.TRJ OPEN READ UNIT 23 FILE NAME DYN2.TRJ TRAJECTORY IREAD 22 NREAD 2 SKIP 100 SET 1 1 SET 9 9999.0 LABEL LOOP TRAJ READ GETE IF 9 LT ?ENER GOTO NEXT SET 8 @1 COOR COPY SET 9 ?ENER LABEL NEXT INCR 1 BY 1 IF 1 LT 1000.5 GOTO LOOP OPEN WRITE CARD UNIT 12 NAME LOWE.CRD WRITE COOR COMP CARD UNIT 12 * structure with the lowest energy * frame number @8 with energy @9 * STOP =================================================================== 3) Copying from one trajectory to another. The operation of this command works in the same mode as the MERGE command, except a variety of CHARMM commands can be executed between reading and writing of frames. EXAMPLES: Create a new trajectory where every frame is minimized for 200 steps. OPEN READ UNIT 22 FILE NAME DYN.TRJ OPEN WRITE UNIT 32 FILE NAME DYN.MIN TRAJECTORY IREAD 22 SKIP 100 IWRITE 32 * minimized trajectory * SET 1 1 LABEL LOOP TRAJ READ MINI ABNR NSTEP 200 TRAJ WRITE INCR 1 BY 1 IF 1 LT 1000.5 GOTO LOOP STOP

Merges or breaks up a trajectory into different numbers of files 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. Another option is to optionally rotate the structure at each frame to least squares fix a reference structure. [Syntax MERGE dynamics trajectories] MERGE [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer] [ VEL ] [OUTPutu unit-number] [NFILE integer] [ DRAW ] [BEGIN integer] [STOP integer] [first-atom-selection] [ ORIEnt [MASS] [WEIGht] [NOROt] [PRINT] second-atom-selection ] Keyword table Option Default Purpose [COOR] COOR Specification of the type of trajectory file. COOR is [VEL ] coordinates; VEL is velocities. [DRAW] Make a CHARMM movie (do not write any files, just display) 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 coordinate sets written to each output merged 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. BEGIN First step number to start reading from STOP Last step number to read first-atom-sel Selection of atoms to include in the output file. ORIEnt Flag to specify best fit rotation and translations. MASS Use mass weighting in best fit. WEIGht Use weighting array for best fit weights. NOROt Only translate in the best fit. PRINT Print the details of best fit second-atom-sel Selection of atoms to use in the best fit. The title of the output trajectory will be copied from the input trajectory.

Reorienting a coordinate trajectory If one is interested in reorienting every set of coordinates found in a dynamics trajectory with respect to some reference structure, one can use the ORIEnt option in conjunction with the MERGe command. The process of reorienting a coordinate trajectory works as follows: A series of files containing the trajectory are assigned to successive units prior to a CHARMM run. The coordinates stored therein are presumed to have been written every NSAVC steps. CHARMM will read each coordinate, select some periodically, reorient them, and write them to successive units where each output file will have a user specified number of coordinates. The following table lists the options involved: Option Default Purpose ORIE .false. Specify that a least squares RMS fit will be done. MASS .false. Use a mass weighting in the fit WEIGH .false. Use the weighting array (wmain) in the fit NOROt .false. Just shift the centers to best fit. PRINt .false. Print what happened to each coordinate set. atom-selection all Select which atom to use in the fit. If atoms were fixed during the dynamics, the new trajectory produced will not have fixed atoms because the rotations applied to each coordinate set will be different thereby yielding different coordinates for the fixed atoms. Fixing the coordinates leads to a large space reductions, so the reorientation process will therefore result in potentially much larger trajectory files. See *note fix: (cons.doc)Fixed Atom.

Computes the RMS difference between two trajectory files and make a matrix of results. Large files should be reduced with the MERGe command before processing this command. RMSDynmics [IREAd unit-number] [JREAd unit-number] [IWRIte unit-number] [BEGIn integer] [STOP integer] [IMAGes] ORIEnt [MASS] [WEIGht] [NOROt] [RMS] atom-selection IREAd int - unit number of the first trajectory file. JREAd int - unit number of the second trajectory file. IWRIte int - Unit for the output matrix. BEGIn int - Starting step number (default: first) STOP int - Ending step number (default: last) IMAGes - Use image atoms for the analysis ORIEnt - Do best fit of structures MASS - Use a mass weighting in best fit. WEIGht - Use the weighting array in best fit. NOROt - Best fit without letting the structures rotate. RMS - Do RMS fit between structures, otherwise, align structures with the axis. atom-selection - Atoms to use in the fitting procedure.

Format or unformat a dynamics trajectory DYNAmics FORMat FIRStunit <unit> NUNIt <int> BEGIn <int> SKIP <int> STOP <int> OUTPut <unit> OFFSet <int> SCALe <int> MODE <FORTRAN-FORMAT> DYNAmics UNFOrmat INPUt <unit> OUTPut <unit> These commands allow to convert binary trajectory files into a machine independent yet compact format and to convert them back into binary files. The defaults for OFFSet, SCALe and MODE are: OFFSet=600, SCALE=10000, and MODE=12Z6. The trajectory is converted into positive integers according to the formula <integer>=INT(<real>+OFFSET)*SCALE). The user has to make sure that all coordinates of the trajectory are within OFFSET angstroms. The precision may be increased by choosing a larger SCALE and FORTRAN-format, e.g. MODE=11Z7 OFFSET=100000. ("Z" is the hexadecimal format and is available on most machines.)

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