#$Id: imd2.dat,v 1.6 JWP Oct 1999 Exp $
TITLE
Equilibration simulation of BEE, at constant pressure
21-5-2001
END
#MINIMISE
#     NTEM    NCYC    DELE    DX0     DXM
#        1      20     0.0001   0.01    0.05
#END
#STOCHASTIC
#NTFR
#0 = set to zero
#1 = set to CFRIC
#2 = set to CFRIC*GAM
#3 = calculate using SUBR. FRIC
#     NTFR     NSFR     NBREF  RCUTF    CFRIC    TEMPSD
#        3      300         6   0.3      91.0     300.0
#END
SYSTEM
#      NPM      NSM 
      512       0
END
START
# values for INIT -- starting procedures in RUNMD.f
#  INIT
#     shake X
#            shake V
# centre of mass motion removal if NTCM=1
#     1   yes    yes   yes
#     2    no    yes   yes
#     3    no     no   yes
#     4    no     no    no
#      NTX     INIT      IG     TEMPI      HEAT  NTXO   BOLTZ
         2        4  210185       0.0   0.00000     1   8.31441E-3
END
STEP
#   NSTLIM         T        DT
     50000       0.0     0.002
END
BOUNDARY
#      NTB    BOX(1)    BOX(2)    BOX(3)      BETA  NRDBOX
         2       0.0       0.0       0.0      90.0       1
END
SUBMOLECULES
#     NSPM  NSP(1.. NSPM)
         1   8
END
TCOUPLE
#      NTT     TEMP0      TAUT
         2     298.15     0.100
        -2     298.15     0.100
         0     298.15     0.100
END
PCOUPLE
#     NTP     PRES0      COMP      TAUP  
        1  0.061020  1.400E-03   0.50000
END
CENTREOFMASS
#   NDFMIN      NTCM      NSCM
         0         0      1000
END
PRINT
#NTPR: print out energies, etc. every NTPR steps
#NTPL: print out C.O.M motion and total energy fitting every NTPL steps
#NTPP: =1 perform dihedral angle transition monitoring
#     NTPR      NTPL      NTPP
      1000      1000         0
END
WRITE
# NTPW = 0 : binary
# NTPW = 1 : formatted
# NTWSE = configuration selection parameter
# =0: write normal trajectory
# >0: chose min energy for writing configurations
#     NTWX     NTWSE      NTWV      NTWE      NTWG      NTPW
       0         0         0         0         0         1
END
SHAKE
#      NTC       TOL
         3    0.0001
END
FORCE
#      NTF array
# bonds    angles    imp.     dihe     charge nonbonded
# H        H         H        H
  0  0     1  1      1  1     1  1     1  1
# NEGR    NRE(1)    NRE(2)    ...      NRE(NEGR)
     1         4096
END
PLIST
#     NTNB      NSNB     RCUTP     RCUTL
         1         5       0.8       1.4
END
LONGRANGE
# EPSRF     APPAK      RCRF
    5.01       0.0       1.4
END
#
POSREST
#     values for NTR
#     0: no position re(con)straining
#     1: use CHO
#     2: use CHO/ ATOMIC B-FACTORS
#     3: position constraining
#      NTR       CHO   NRDRX
         0     2.5E4       1
END
#
#DISTREST
#     NTDR
#     0 : no distance restraining
#     -1,1 : use CDIS
#     -2,2:  use W0*CDIS
#     NTDR < 0 : time averaging
#     NTDR > 0 : no time averaging
# NRDDR = 1: read in time averaged distances (for continuation run)
# NRDDR = 0: don't read them in, recalc from scratch
#     NTDR      CDIS       DR0     TAUDR     NRDDR
#        0    1000.0   1.00000      10.0         0
#END
#DIHEREST
# values for NTDLR
# 0: no dihedral angle restraining
# 1: use CDLR
# 2: use CDLR * CPLR
#    NTDLR      CDLR
#        0       0.1
#END
#J-VAL
# values for NTJR
#     0: no J-value restraining
#     -1,1: use CJR*(a*cos^^2 + b*cos + c)
#     -2,2: use CJR*CPJR*(a*cos^^2 + b*cos + c)
#     NTJR < 0: time averaging
#     NTJR > 0: no time averaging
#---
# values for NTJRH
#    0: use half harmonic potential
#    1: use harmonic potential
# values for NRDJR
#    0: start from initial values
#    1: read in time averages (for continuation run)
#     NTJR     NTJRH       CJR     TAUJR     NRDJR
#        0         1      10.0      10.0         0 
#END
#---------
#LOCALELEVATION
# NTLE
# 0: off
# 1: gaussian potential energy function
# 2: inverse quadratic energy fuction
#--
# NRDLE
# 0: don't read in memory
# 1: read in memory (for continuation run)
#   NTLE   CWLE  NRDLE
#      0    2.5      0
#END
#---------
#FOURDIM
#  NT4DIM	meaning
#	0	perform 3D simulation
#	>0	perform 4D simulation
#	1	use CW4DA
#	2	use CW4DA*C4D
#---
# NT4XI determines initial coordinates and
# velocities in the 4'th dimension
#		init coords	init velocities
#	1	0		max dist
#	2	boltz		set to 0
#	3	read coords	max dist
#	4	read coords and velocities from unit 'XVI' (for continuation run)
#---
# NT4XO : 1 write out 4'th dimensional data to trajectory
#       : 0 write out only 3 dimensions to trajectory
#---
#  NT4DIM	CW4DA	TEMP4I	NDFMI4   NT4XI NT4XO
#       0      5000.0     30.0	     0       1     0
#------
# temperature coupling in the 4'th dimension
#    NTT4      TEMP04	  TAUT4
#       1        30.0   0.10000
# NTCW4D 0: constant reference temperature and using CW4DA as force constant
# 1: reference temperature is linearly changed from TEMP04 to TEMP0B,
#    force constant is changed from CW4DA to CW4DB over NSTLIM steps.
#  NTCW4D	CW4DB    TEMP0B
#       0        10.0     300.0
# NTF4: 4D force terms: 0 = perform in 3D, 1 = perform in 4D
#     	bond/shake
#               bond angle
#                       dihedral
#                               non-bonded
#                                   	dist rest
#                                      		4d harm osc
#       0       0       0       1       0       1
#END
#PERTURB
# NTG: 0 no perturbation is applied
#    : 1 calculate dV/dRLAM perturbation
#    : 2 calculate dV/dRMU perturbation
#    : 3 calculate both derivatives
#      NTG     NRDGL     RLAM     DLAMT        RMU   DMUT
#         1         0      0.5   0.00000    0.00000   0.00
#   ALPHLJ     ALPHC     NLAM       MMU
#       2.0    0.0005        1         1
#END
#-------
#PATHINT
# restrictions for PI
# topology must contain bead information
# pathint in 4D is disabled
# pathint and perturbation not allowed
# a warning is written out if the temperature at discretization
# is not the same as the MD run is performed at.
#
# values or NTPI
#     0: no path integral calculation
#     1: path integral calculation
#---
# NTPI
#    0
#END