tranal.in_help

分子动力学模拟程序

!  Commentaries to the input file for program "tranal"
!
!  Trajectory files may be in binary MDynaMix format,"XMOL" format, 
!  of PDB format (converted from GROMACS) numbered .001,002,003,...
!  Atoms must be grouped in molecules, ecah molecule type after another
!
!  Example: Analys of trajectories from MD simulations of NaCl aqueous solution
!
!  The input file must be in strict NAMELIST format
!  All commentaries must be removed!
!
 &INPUT 
!   General parameters:
 NFORM='MDYN'         ! Format of trajectory: MDYN, XMOL or PDBT
 FNAME='../4nacl',    ! file name of trajectory files 
                      ! (without extensions 001, 002,...)
 NFBEG=1,             ! first trajectory file to be analysed
 NFEND=40,            ! last trajectory file
 PATHDB='../moldb',   ! path to molecular data base
 IPRINT=4,            ! level of output
!    System
 NTYPES=3,            ! number of molecule's types
 NAMOL='H2O','Na+_SD','Cl-_SD',   ! names of molecules 
                                  ! (the same as in MD simulations)
		      ! .mol from MDynaMix files must be present,
		      !  at least their first part with atom coordinates
 NSPEC=256,5,5        ! number of molecules of each type
 BOXL=22.4,           ! box sizes (needed only for XMOL trajectory format)
 BOYL=22.4,
 BOZL=22.4,
!
!  Calculation of spatial distribution /orientational distrib. functions
!
 LORIENT=.f.,        ! set .true. to calculate SDF
 NDUP=2,             ! number of equiv. atom sites "to"
 NOI=1,              ! number of equiv. atom sites "from"
 IO1=1,              !  These three are arrays of size NOI. 
 IO2=2,              !  They define local coordinate system
 IO3=3,              !  IO1 - center; X- axis is mediana of 3-1-2 angle
                     !  Z axis is perpendicular to 1-2-3 plane
 ISOR=2,3,           !  for which sites calculate SDF - array of size NDUP
                     !  (here: 2 and 3 are H atoms of water molecules
 IPROC=0,            !  Which SDF to calculate: 
                     !  0 - normal; result is 3D SDF in ASCII format for 
                     !      GOpenMol program
                     !      (http://laaksonen.csc.fi./gopenmol/gopenmol.html) 
                     !  1,2,3 - 2D projections of SDF in XY, YZ and XZ planes
                     !  this is old feature may be notworking now
                     !  -1; 4 - these parameters may be used to
                     !  analyse SDFs around DNA - not commented
                     !  So: keep IROC=0
                     !
 FSET='h2o.sit'      !  File defining how to create ".crd" file containing
                     !  average structure of the "from" molecule 
                     !  (explaived below)
 filori='h2oH_spc.ori',  ! file with resulting SDF
 fcrd='h2o.crd',     !  File with average structure of the "from" molecule in
                     !  local coordinate system defined by IO1,IO2,IO3
                     !  The file is written in PDB / CHARMM format
 NOMX=60,            !  Number of "bins" for SDF in X direction
 NOMY=60,            !          "                   Y
 NOMZ=60,            !          "                   Z
 RXMAX=6.,           !  Half-size of region to calculate SDF in X-direction
 RYMAX=6.,           !          "                   Y
 RZMAX=6.,           !          "                   Z
 ZB=0.,              !    for 2D SDF (IPROC=1,2,3): 
                     !    the third corrdinate defining the plane
 DZB=0.2,            !    thickness of the layer to calculate 2D SDF
!
!  Parameters to calculate 3-body distribution functions
!  (Actually distribution of the third particle is calculated if
!  the fisrt two particles are fixed at given distance)
!
 LCOR3=.f.,         ! calculate 3-body distribution       
 NDUR=1,            ! keep this (too long to explain...)
!  these are arrays of size NDUP (see above)
 IS1=1,             ! first site
 IS2=4,             ! second site
 IS3=1,             ! third site
 AMPL=0.2,0.5,0.75,1.,1.5,2.,3.,5.,7.,10.,   ! amplitudes defining intensities
                    ! to drawdensity plot
 fil3cor='Na_O.ps', ! file name for 3-body cor. function
 RMAXX=7.,          ! size of the region to calculate 3-body cor. function
 RMAXY=7.,          !
 NRX=200,           ! number of "bins" to calculate 3-body c.f.
 NRY=100,           ! (note: size in Y direction is twice less because of
                    ! symmetry)
 RB12=2.36,         ! distance between the first and second sites
 D12=0.2,           ! allowed deviation from this distance
!
!  Calculation of RDFs
!
 LRDF=.f.,           ! .true. to calculate RDFs
 NA=200,             ! number of "bins" for RDF
 RDFCUT=10.,         ! RDF - cutoff
 FIRDF='h2o.rdi',    ! Input file defining which RDF calculate. It has the
                     ! same format is the last part of the input file
                     ! for MDynamix program defining calculation of RDFs
 FORDF='h2o_out.rdf' ! Output file with RDF-s
!
!  calculation of diffusion coefficients
!
 LDIFF=.t.,            ! calciulate diffusion coefficients
 fildif='Na_h2o.diff', ! file with results 
 IDF=2,                ! for which molecule (type number!) we want calculate
                       ! diffusion
 DTT=2.d-13,           ! Time step to calculate RMS displacement
 NTT=1000,             ! Number of steps to calculate RMS displacement
                       ! (total time to cal鯿ulate RMSD is DTT*NTT) 
 ICNT=10,              ! If we want to keep track of a specific molecule
                       ! (only on screen output if IPRINT > 5)
 ISTEP=4,              ! Take configurations only each "ISTEP" step
                       ! from the trajectory file
                       ! (it is good to choose ISTEP*TRST=DTT, where
                       ! TRST is the time step in the trajectory files)
 BREAKM=10.            ! Max allowed break in trajectory for diffusion
                       ! computations
!
!  calculation of residence (life) tomes
!
 LRES=.f.,             ! calculate residence time
 filres='Ow_Na.res',   ! result on residence time calculations
 NR1=1,               ! number of equivalent "from" sites
 NR2=1,               ! number of equivalent "to" sites
 IR1=4,               ! "from" sites (array of size NR1)
 IR2=1,               ! "to" sites (array of size NR2)
 RRN=0.,              ! closest distance
 RRX=3.2,             ! maximum distance
                      ! life time is calculated for the distance 
                      ! between the to sites to be between RRN and RRX
                      ! while calculating residence time, we count
 RRD=0.25,            ! "go in" - if distance < RRX-RRD
                      ! "go out" - if distance > RRX+RRD
 TTER=2.,             ! In the first definition of residence time
                      ! (see A.P.Lyubartsev, A.Laaksonen, J.Phys.Chem.,
                      ! 100,16410 (1996)) the time to be in "bound" state
                      ! is not interrupted if the distance between the sites 
                      ! exceed RRX during less then TTER ps. In the third
                      ! definition (exponent decay) the exponent decay is 
                      ! calculated starting from TTER ps.
 NITT=1000,           ! Number of (time) points to calculate probability 
                      ! to dispupt "bound" state
 TIMM=500.,           ! Total time (in ps) to calculate above
!
!  Calculate distribution of torsion angles
!
 LANG=.f.,             ! calculate torsion angles
 NAA=72,               ! number of "bins" to calculate this distribution
 fangl='dna.tors',     ! file defining for wich torsion angles 
                       ! calculate distribution
 ftor='NaDNAtor.lst',  ! file with results
!
!  Calculation or order parameter relative Z axis
!
 LORD=.t.,            ! Calculate order parameters
 FORDIN="order.in"    ! Input file for order parameter calculations
 FORD="order.out",    ! Name of ouput file
!
!  Calculate average structure and RMS deviation 
!  (work only for DNA-like system)
!
 LRMS=.f.,
 IMAC=1,
 frms='DNA_RMS.lst',
!
!  Time autocorrelation functions
!
 LTCF=.t., 
 LVEL=.t.,           ! whether velocities included into trajectory files
                     ! otherwise, they will be calculated from 
                     ! coordinates which is very unreliable
 FILTCF="Na_VACF.tcf"    ! file name for TCF output
 N1=1,0,0,           ! sites defining reorientational TCF
 N2=2,1,1, 
 ITCF=1,0,0,0,1,1,2,2,2,0,0,0,  ! which TCF to compute 
                                ! (the same as in MDynaMix program)
 NSTEG=1000,                  ! number of steps for TCF calculations
 DTCF=0.005,                  ! time step for TCF calculations
 &END
!

...

Format of .sit file for drawing the SDF (not needed if LORIENT=.f.)

.sit fole defines average coordinates of which atoms are calculated and 
stored in the .crd file. This file containes atom coordinates for the 
molecule, around wihich the SDF is calculated.

First line - number of atoms in the .crd file (may be less that total 
atoms in the molecule)
Then one line for each atom with 2 numbers: symmetry number (1,2 or 3)
and "site number" exactly as in the MD program.
Example: 
Let we have mixture H2O (1st type) and CH3OH (2nd type); atom ordering 
see in the corresponding .mol files

For H2O:
-----
3
1  1
2  2
1  3
------

2 in the first column, 3 line means that that the next atom (H) is 
identical with this atom 

For CH3OH  (site numbers from 4 to 9 in this case)

-------
6
1  4
1  5
1  6
3  7                
2  8
1  9