amber动力学常用参数说明个人日记2009-05-08 19:32:18 阅读130 评论1 字号：大中小订阅IMIN Flag to run minimization=0 No minimization (only do molecular dynamics;default)= 1 Perform minimization (and no molecular dynamics)=5 Read in a trajectory for analysis.NTX Option to read the initial coordinates, velocities and box size from the "inpcrd" file. The options 1-2 must be used when one is starting from minimized or model-built coordinates. If an MD restrt file is used as inpcrd, thenoptions 4-7 may be used.= 1 X is read formatted with no initial velocity information (default)= 2 X is read unformatted with no initial velocity information= 4 X and V are read unformatted.= 5 X and V are read formatted; box information will be read if ntb>0. The velocity information will only be used if irest=1.= 6 X, V and BOX(1..3) are read unformatted; in other respects, this is the same as option "5".=7 Same as option "5"; only included for backward compatibility with earlier versions of Amber. IREST Flag to restart the run.= 0 Noeffect (default)= 1 restart calculation. Requires velocities in coordinate input file, so you also may need to reset NTX if restarting MD.NTRX Format of the Cartesian coordinates for restraint from file "refc". Note: the program expects file "refc" to contain coordinates for all the atoms in the system. A subset for the actual restraints is selected by restraintmask in the controlnamelist.= 0 Unformatted (binary) form= 1 Formatted (ascii, default) formNTPR Every NTPR steps energy information will be printed in human-readable form to files "mdout" and "mdinfo". "mdinfo" is closed and reopened each time, so it always contains the most recent energy and temperature. Default 50.NTWR Every NTWR steps during dynamics, the "restrt" file will be written, ensuring that recovery from a crash will not be so painful. In any case, restrt is written ev ery NSTLIM steps for both dynamics and minimization calculations. If NTWR<0, a unique copy of the file, restrt_nstep, is written every abs(NTWR) steps. This option is useful if for example one wants to run free energy perturbations from multiple starting points or save a series of restrt files for minimization. Default 500.NTF Force evaluation. Note: If SHAKE is used (see NTC), it is not necessary to calculate forces for the constrained bonds.= 1 complete interaction is calculated (default)= 2 bond interactions involving H-atoms omitted (use with NTC=2)= 3 all the bond interactions are omitted (use with NTC=3)= 4 angle involving H-atoms and all bonds are omitted= 5 all bond and angle interactions are omitted= 6 dihedrals involving H-atoms and all bonds and all angle interactions are omitted= 7 all bond, angle and dihedral interactions are omitted= 8 all bond, angle, dihedral and non-bonded interactions are omittedNTB Periodic boundary. If NTB .EQ. 0 then a boundary is NOT applied regardless of any boundary condition information in the topology file. The value of NTB specifies whether constant volume or constant pressure dynamics will be used. Options for constant pressure are described in a separate section below.= 0 no periodicity is applied and PME is off= 1 constant volume (default)= 2 constant pressureIf NTB .NE. 0, there must be a periodic boundary in the topology file. Constant pressure is not used in minimization (IMIN=1, above). For a periodic system, constant pressure is the only way to equilibrate densityif the starting state is not correct. For example, the solvent packing scheme used in LEaP can result in a net void when solvent molecules are subtracted which can aggregate into "vacuum bubbles" in a constant volume run. Another potential problem are small gaps at the edges of the box. The upshot is that almost every system needs to be equilibrated at constant pressure (ntb=2, ntp>0) to get to a proper density. But be sure to equilibrate first (at constant volume) to something close to the final temperature, before turning on constant pressure.CUT This is used to specify the nonbonded cutoff, in Angstroms. For PME, the cutoff is used to limit direct space sum, and the default value of 8.0is usually a good value. When igb>0, the cutoff is used to truncate nonbonded pairs (on an atom-by-atom basis); here a larger value than the default is generally required. A separate parameter (RGBMAX) controls the maximum distance between atom pairs that will be considered in carrying out the pairwise summation involved in calculating the effective Born radii, see the generalized Born section below.IBELLY Flag for belly type dynamics.= 0 No belly run (default).= 1 Belly run. A subset of the atoms in the system will be allowed to move, and the coordinates of the rest will be frozen. The moving atoms are specified bellymask. This option is not available when igb>0. Note also that this option does not provide any significant speed advantage, and is maintained primarily for backwards compatibilitywith older version of Amber. Most applications should use the ntr variable instead to restrain parts of the system to stay close to some initial configuration.NTR Flag for restraining specified atoms in Cartesian space using a harmonic potential. The restrained atoms are determined by the restraintmask string. The force constant is given by restraint_wt. The coordinates are read in "restrt" format from the "refc" file (see NTRX, above). = 0 No position restraints (default) = 1 MD with restraint of specified atomsMAXCYC The maximum number of cycles of minimization. Default 1.NCYC If NTMIN is 1 then the method of minimization will be switched from steepest descent to conjugate gradient after NCYC cycles. Default 10.NSTLIM Number of MD-steps to be performed. Default 1.TEMP0Reference temperature at which the system is to be kept, if ntt > 0. Note that for temperatures above 300K, the step size should be reduced since increased distance traveled between evaluations can lead to SHAKE and other problems. Default 300.TEMPI Initial temperature. For the initial dynamics run, (NTX .lt. 3) the velocities are assignedfrom a Maxwellian distribution at TEMPI K. If TEMPI = 0.0, the velocities will be calculated from the forces instead. TEMPI has no effect if NTX .gt. 3. Default 0.0.NTT Switch for temperature scaling. Note that setting ntt=0 corresponds to the microcanonical (NVE) ensemble (which should approach the canonical one for large numbers of degrees of freedom). Some aspects of the "weak-coupling ensemble" (ntt=1) have been examined, and roughly interpolate between the microcanonical and canonical ensembles [63]. The ntt=2 and 3 options correspond to the canonical (constant T) ensemble. The ntt=4 option is included for historical reasons, but does not correspond to any of the traditionalensembles.= 0 Constant total energy classical dynamics (assuming that ntb<2, as should probably always be the case when ntt=0).= 1 Constant temperature, using the weak-coupling algorithm [64]. A single scaling factor is used for all atoms. Note that this algorithm just ensures that the total kinetic energy is appropriate for the desired temperature; it does nothing to ensure that the temperature is even over all parts of the molecule. Atomic collisions should serve to ensure an even temperature distribution, but this is not guaranteed, and can be a particular problem for generalized Born simulations, where there are no collisions with solvent. Other temperature coupling options (especially ntt=3) should probably be used for generalized Born simulations.= 2 Andersen temperature coupling scheme [65], in which imaginary "collisions" randomize the velocities to a distribution corresponding to temp0 every vrand steps. Note that in between these "massive collisions",the dynamics is Newtonian. Hence, time correlation functions (etc.) can be computed in these sections, and the results averaged over an initial canonical distribution. Note also that too high a collision rate (too small a value of vrand) will slow down the speed at which the molecules explore configuration space, whereas too low a rate means that the canonical distribution of energies will be sampled slowly. A discussion of this rate is given by Andersen [66].= 3 Use Langevin dynamics with the collision frequency γ given by gamma_ln, discussed below. Note that when γ has its default value of zero, this is the same as setting ntt = 0.GAMMA_LN The collision frequency γ , in ps-1, when ntt = 3. A simple Leapfrog integrator is used to propagate the dynamics, with the kinetic energy adjusted to be correct for the harmonic oscillator case [67,68]. Note that it is not necessary that γ approximate the physical collision frequency. In fact, it is often advantageous, in terms of sampling or stability of integration, to use much smaller values. Default is 0NTP Flag for constant pressure dynamics. This option should be set to 1 or 2 when Constant Pressure periodic boundary conditions are used (NTB = 2).= 0 Used with NTB not = 2 (default); no pressure scaling= 1 md with isotropic position scaling= 2 md with anisotropic (x-,y-,z-) pressure scaling: this should only be used with orthogonal boxes (i.e. with all angles set to 90). Anisotropic scaling is primarily intended for non-isotropic systems, such as membrane simulations, where the surface tensions are different in different directions; it is generally not appropriate for solutes dissolved in water.NTC Flag for SHAKE to perform bond length constraints [70]. (See also NTF in the Potential function section. In particular, typically NTF = NTC.) The SHAKE option should be used for most MD calculations. The size of the MDtimestep is determined by the fastest motions in the system. SHAKE removes the bond stretching freedom, which is the fastest motion, and consequently allows a larger timestep to be used. For water models, a special "three-point" algorithm is used [71]. Consequently, to employ TIP3P set NTF = NTC = 2. Since SHAKE is an algorithm based on dynamics, the minimizer is not aware of what SHAKE is doing; for this reason, minimizations generally should be carried out without SHAKE. One exception is short minimizations whose purpose is to remove bad contacts before dynamics can begin.= 1 SHAKE is not performed (default)= 2 bonds involving hydrogen are constrained= 3 all bonds are constrained (not available for parallel runs in sander)。