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Release66:Format of MD Files

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Format of fragment file
Card Format Description
I-1-1 a1 $ or # comments to describe fragment
I-2-1 i5 number of atoms in the fragment
I-2-2 i5 number of parameter sets
I-2-3 i5 default parameter set
I-2-4 i5 number of z-matrix definition
For each parameter set one card I-3
I-3-1 a residue name for parameter set
For each atom one deck II
II-1-1 i5 atom sequence number
II-1-2 a6 atom name
II-1-3 a5 atom type
II-1-4 a1 dynamics type
blank : normal
D : dummy atom
S: solute interactions only
Q : quantum atom
other : intramolecular solute interactions only
II-1-5 i5 link number
0: no link
1: first atom in chain
2: second atom in chain
3 and up: other links
II-1-6 i5 environment type
0: no special identifier
1: planar, using improper torsion
2: tetrahedral, using improper torsion
3: tetrahedral, using improper torsion
4: atom in aromatic ring
II-1-7 i5
II-1-8 i5 charge group
II-1-9 i5 polarization group
II-1-10 f12.6 atomic partial charge
II-1-11 f12.6 atomic polarizability
For each additional parameter set on card II-2
II-2-1 11x,a6 atom type
II-2-2 a1 dynamics type
blank : normal
D : dummy atom
S : solute interactions only
Q : quantum atom
other : intramolecular solute interactions only
II-2-7 25x,f12.6 atomic partial charge
II-2-8 f12.6 atomic polarizability
Any number of cards in deck III to specify complete connectivity
III-1-1 16i5 connectivity, duplication allowed
One blank card to signal the end of the connectivity list
For each z-matrix definition one card IV
IV-1-1 i5 atom i
IV-1-2 i5 atom j
IV-1-3 i5 atom k
IV-1-4 i5 atom l
IV-1-5 f12.6 bond length i-j
IV-1-6 f12.6 angle i-j-k
IV-1-7 f12.6 torson i-j-k-l


Format of segment file (1 of 7)
Card Format Description
I-0-1 # lines at top are comments
I-1-1 a1 $ to identify the start of a segment
I-1-2 a10 name of the segment, the tenth character
N: identifies beginning of a chain
C: identifies end of a chain
blank: identifies chain fragment
M: identifies an integral molecule
I-2-1 f12.6 version number
I-3-1 i5 number of atoms in the segment
I-3-2 i5 number of bonds in the segment
I-3-3 i5 number of angles in the segment
I-3-4 i5 number of proper dihedrals in the segment
I-3-5 i5 number of improper dihedrals in the segment
I-3-6 i5 number of z-matrix definitions
I-3-7 i5 number of parameter sets
1-3-8 i5 default parameter set
For each parameter set one card I-4
I-4-1 f12.6 dipole correction energy


Format of segment file (2 of 7)
Card Format Description
For each atom one deck II
II-1-1 i5 atom sequence number
II-1-2 a6 atom name
II-1-3 i5 link number
II-1-4 i5 environment type
0: no special identifier
1: planar, using improper torsion
2: tetrahedral, using improper torsion
3: tetrahedral, using improper torsion
4: atom in aromatic ring
II-1-5 i5
II-1-6 i5 charge group
II-1-7 i5 polarization group
For each parameter set one card II-2
II-2-1 5x,a5 atom type
II-2-2 a1 dynamics type
blank : normal
D : dummy atom
S : solute interactions only
Q : quantum atom
other : intramolecular solute interactions only
II-2-3 f12.6 atomic partial charge in e
II-2-4 f12.6 atomic polarizability 4πεoinnm3


Format of segment file (3 of 7)
Card Format Description
For each bond a deck III
III-1-1 i5 bond sequence number
III-1-2 i5 bond atom i
III-1-3 i5 bond atom j
III-1-4 i5 bond type
0: harmonic
1: constrained bond
III-1-5 i5 bond parameter origin
0: from database, next card ignored
1: from next card
For each parameter set one card III-2
III-2-1 f12.6 bond length in nm
III-2-2 e12.5 bond force constant in kJnm2mol − 1


Format of segment file (4 of 7)
Card Format Description
For each angle a deck IV
IV-1-1 i5 angle sequence number
IV-1-2 i5 angle atom i
IV-1-3 i5 angle atom j
IV-1-4 i5 angle atom k
IV-1-5 i5 angle type
0: harmonic
IV-1-6 i5 angle parameter origin
0: from database, next card ignored
1: from next card
For each parameter set one card IV-2
IV-2-1 f10.6 angle in radians
IV-2-2 e12.5 angle force constant in kJmol − 1


Format of segment file (5 of 7)
Card Format Description
For each proper dihedral a deck V
V-1-1 i5 proper dihedral sequence number
V-1-2 i5 proper dihedral atom i
V-1-3 i5 proper dihedral atom j
V-1-4 i5 proper dihedral atom k
V-1-5 i5 proper dihedral atom l
V-1-6 i5 proper dihedral type
0: Ccos(mφ − δ)
V-1-7 i5 proper dihedral parameter origin
0: from database, next card ignored
1: from next card
For each parameter set one card V-2
V-2-1 i3 multiplicity
V-2-2 f10.6 proper dihedral in radians
V-2-3 e12.5 proper dihedral force constant in kJmol − 1


Format of segment file (6 of 7)
Card Format Description
For each improper dihedral a deck VI
VI-1-1 i5 improper dihedral sequence number
VI-1-2 i5 improper dihedral atom i
VI-1-3 i5 improper dihedral atom j
VI-1-4 i5 improper dihedral atom k
VI-1-5 i5 improper dihedral atom l
VI-1-6 i5 improper dihedral type
0: harmonic
VI-1-7 i5 improper dihedral parameter origin
0: from database, next card ignored
1: from next card
For each parameter set one card VI-2
VI-2-1 3x,f10.6 improper dihedral in radians
VI-2-2 e12.5 improper dihedral force constant in kJmol − 1


Format of segment file (7 of 7)
Card Format Description
For each z-matrix definition one card VII
VII-1-1 i5 atom i
VII-1-2 i5 atom j
VII-1-3 i5 atom k
VII-1-4 i5 atom l
VII-1-5 f12.6 bond length i-j
VII-1-6 f12.6 angle i-j-k
VII-1-7 f12.6 torson i-j-k-l


Format of sequence file
Card Format Description
I-1-1 a1 $ to identify the start of a sequence
I-1-2 a10 name of the sequence
Any number of cards 1 and 2 in deck II to specify the system
II-1-1 i5 segment number
II-1-2 a10 segment name, last character will be determined from chain
II-2-1 a break to identify a break in the molecule chain
II-2-1 a molecule to identify the end of a solute molecule
II-2-1 a fraction to identify the end of a solute fraction
II-2-1 a5 link to specify a link
II-2-2 i5 segment number of first link atom
II-2-3 a4 name of first link atom
II-2-4 i5 segment number of second link atom
II-2-5 a4 name of second link atom
II-2-1 a solvent to identify solvent definition on next card
II-2-1 a stop to identify the end of the sequence
II-2-1 a6 repeat to repeat next ncard cards ncount times
II-2-2 i5 number of cards to repeat (ncards)
II-2-3 i5 number of times to repeat cards (ncount)
Any number of cards in deck II to specify the system


Format of trajectory file
Card Format Description
I-1-1 a6 keyword header
I-2-1 i10 number of atoms per solvent molecule
I-2-2 i10 number of solute atoms
I-2-3 i10 number of solute bonds
I-2-4 i10 number of solvent bonds
I-2-5 i10 number of solvent molecules
I-2-6 i10 precision of the coordinates. 0=standard, 1=high
For each atom per solvent molecule one card I-3
I-3-1 a5 solvent name
I-3-2 a5 atom name
For each solute atom one card I-4
I-4-1 a5 segment name
I-4-2 a5 atom name
I-4-3 i6 segment number
I-4-4 i10 solute atom counter
I-4-5 i5 integer 1
For each solvent bond one card I-5
I-5-1 i8 atom index i for bond between i and j
I-5-2 i8 atom index j for bond between i and j
For each solute bond one card I-6
I-6-1 i8 atom index i for bond between i and j
I-6-2 i8 atom index j for bond between i and j
For each frame one deck II
II-1-1 a5 keyword frame
II-2-1 f12.6 time of frame in ps
II-2-2 12.6 temperature of frame in K
II-2-3 e12.5 pressure of frame in Pa
II-2-4 a10 date
II-2-5 a10 time
II-3-1 f12.6 box dimension x
II-3-2 12x,f12.6 box dimension y
II-3-3 24x,f12.6 box dimension z
II-4-1 l1 logical lxw for solvent coordinates
II-4-2 l1 logical lvw for solvent velocities
II-4-3 l1 logical lfw for solvent forces
I-4-4 l1 logical lpw for solvent induced dipoles
II-4-5 l1 logical lxs for solute coordinates
II-4-6 l1 logical lvs for solute velocities
II-4-7 l1 logical lfs for solute forces
II-4-8 l1 logical lps for solute induced dipoles
II-4-5 i10 number of solvent molecules
II-4-6 i10 number of solvent atoms
II-4-7 i10 number of solute atoms
For each solvent molecule one card II-5 for each atom, if standard precision
II-5-1 3f8.3 solvent atom coordinates, if lxw or lvw
II-5-4 3f8.3 solvent atom velocities, if lvw
II-5-7 3f8.1 solvent atom forces, if lfw
For each solute atom one card II-6 for each atom, if standard precision
II-6-1 3f8.3 solute atom coordinates, if lxs or lvs
II-6-4 3f8.3 solute atom velocities, if lvs
II-6-7 3f8.1 solute atom forces, if lfs
For each solvent molecule one card II-5 for each atom, if high precision
II-5-1 3e12.6 solvent atom coordinates, if lxw or lvw
II-5-4 3e12.6 solvent atom velocities, if lvw
II-5-7 3e12.6 solvent atom forces, if lfw (on new card if both lxw and lvw)
For each solute atom one card II-6 for each atom, if high precision
II-6-1 3e12.6 solute atom coordinates, if lxs or lvs
II-6-4 3e12.6 solute atom velocities, if lvs
II-6-7 3e12.6 solute atom forces, if lfs (on new card if both lxs and lvs)


Format of free energy file
Card Format Description
For each step in λ one deck I
I-1-1 i7 number nderiv of data summed in derivative decomposition array deriv
I-1-2 i7 length ndata of total derivative array drf
I-1-3 f12.6 current value of λ
I-1-4 f12.6 step size of λ
I-2-1 4e12.12 derivative decomposition array deriv(1:24)
I-3-1 4e12.12 total derivative array dfr(1:nda)
I-4-1 i10 size of ensemble at current λ
I-4-2 e20.12 average temperature at current λ
I-4-3 e20.12 average exponent reverse perturbation energy at current λ
I-4-4 e20.12 average exponent forward perturbation energy at current λ


Format of root mean square deviation file
Card Format Description
For each analyzed time step one card I-1
I-1-1 f12.6 time in ps
I-1-2 f12.6 total rms deviation of the selected atoms before superimposition
I-1-3 f12.6 total rms deviation of the selected atoms after superimposition
II-1-1 a8 keyword analysis
For each solute atom one card II-2
II-2-1 a5 segment name
II-2-2 a5 atom name
II-2-3 i6 segment number
II-2-4 i10 atom number
II-2-5 i5 selected if 1
II-2-6 f12.6 average atom rms deviation after superimposition
III-1-1 a8 keyword analysis
For each solute segment one card III-2
III-2-1 a5 segment name
III-2-2 i6 segment number
III-2-3 f12.6 average segment rms deviation after superimposition


Format of property file
Card Format Description
1 i7 number nprop of recorded properties
I-1-2 1x,2a10 date and time
For each of the nprop properties one card I-2
a50 description of recorded property
For each recorded step one deck II
II-1-1 4(1pe12.5) value of property