mdee.in_help

分子动力学模拟程序

#  Commentaries to the input file for mdee v 4.4 program
#  The true input must be in NAMELIST format
#  (this help file with commentaries can not be run as an input)
#
#  This is a sample for calculation of solvation free energy
#  of CH4 (OPLS) in water (SPC)  
#
#  For more information (description of molecular files .mol etc)
#  see manual to MDynaMix code
#  http://www.fos.su.se/physical/sasha/md_prog.html
#

 &INPUT
#
# General parameters:
#
 FNAME='ch4_h2o',     ! file name for restart file
 LRST= .t.,           ! .t. - read restart file, .f. - new run
 LDMP= .TRUE.,        ! .t. - dump restart file
 LCHECK= .f.,         ! .f. - run simulations; .t. - only check results or
                        check input
 IPRINT=  5,          ! level of output (from 2 to 9)
#
#  Simulated system
#
 NTYPES=  2,          ! number of molecules types 
 NSPEC=  255,1,0,0,   ! number of molecules of each types
 IEE=1,0,             !  1 - for "normal" molecules; 0 - for molecules which 
                         will be deleted/inserted
 NAMOL= 'H2O','CH4',' ',' ',' ',     !  names of molecules
                 files H2O.mol, CH4.mol must be present in directory PATHDB 
 PATHDB='/home/sasha/md/moldb',   ! name of directory containing .mol files
#
#   MD Simulation parameters
#
 NSTEPS=270000,       ! number of MD steps
 DT=2.d-15,           ! (long) time step
 NFREQ=10,            ! short time steps in one long 
 NAVER=10000,         ! number of steps for intermediate averaging
 IAVER=5,             ! output each IAVER step if IPRINT=5
 ICHNB=10,            ! number of (long) steps between recalculation
                        of the list of meighbours
 NDUMP=5000,          ! dump restart file after  NDUMP steps
 IHIST=3,             ! 
 LNVT= .t.,           ! constant-temperature (Nose) MD
 QT=  30.,            ! termostat relaxation time (fs)
 LSCTD=.f.,           ! separate pressure control for each molecule specii 
                        (may be not good for EE)
 LNPT=.t.,            ! constant pressure MD (LNVT must be also .true.)
 LSEP=.f.,            ! separate pressure control in each direction
 QPR=700.,            ! barostat relaxation time 
 TRTEMP=298.D0,       ! temperature (K)
 TPRES=1.,            ! pressure (atm)
 RHO=  1.D0,          ! density (if any of box sizes is zero)
 BOXL=  0.D0,         ! box sizes
 BOYL=  0.D0,
 BOZL=  0.D0,
 RCUT=  0.D0,         ! Cut-off(A), BOXL/2 if zero
 SHORT=5.,            ! Cut-off of short-range forces, recalculated each 
                        short time step
 ALPHA = 2.8          ! Ewald parameters (see MDynaMix manual)
 FEXP = 7.
 LCHP=.f.,            ! Change density at restart according to the input file
                        (if .f. - take from the restart file)
 LSHEJK= .f.,         ! SHAKE algorithm (constraint dynamics) with a single
                        time step
                        otherwise - flexible models, double time step 
 TOLER=1.d-4,         ! Tolerance parameter for SHAKE
#
#  Details of the force field (for each molecule type):
#
 C14EL=  0.0D0,0.0D0,0.0D0,0.,0.,   !  Scaling factors for 1-4 electrostatic 
                                                     interactions
 C14LJ=  0.0D0,0.0D0,0.0D0,0.,0.,   !  for Lennard-Jones interactions
 IPOT=  2,0,0,0,0,                  !  Potential type: 0 - all cases
                                        2 - flexible SPC water model
#
#  Startup:
#
 ICHECK=1,            !  0 - read coordinates from input file *.inp 
                             written in XMOL format
                         1 - Start from FCC lattice 
#
#  Expanded ensemble 
#
 L0AVS= .t.,        ! set accumulated averages to zero (except the
                      probability distribution over subensembles)
 LECH=.t.,          ! change EE parameters at restart 
                        (otherwise, they will be taken from the restart file) 
 NE=12,             ! number of subensembles
 ME0=9,             ! start from this subensemble - at startup, if if the
                      number of subensembles was changed
 NCEE=5,            ! attempts to change subensemble are made after NCEE steps 
 PLOW=0.001,        ! while calculating new biasing factors ita, 
                      disregard probabilities below this 
 LXMOL=.t.,         ! write final configuration in XMOL format
 $end               ! end of NAMELIST section of input
#
#  Expanded ensemble parameters ( read using free format )
#
#  alpha(m)  ita(m) 
1.           2.8
0.8          3.6
0.6          4.
0.4          4.6
0.2          5.2
0.1          5.8
0.03         5.5
0.01         4.4
0.003        3.3
0.001        2.6
0.0001       1.2
0.           0.