17 Format_of_MD_Files

Edoardo Aprà edited this page 2025-05-30 16:32:09 -07:00

Table of Contents

• Format of MD files
• Format of fragment file
• Format of segment file (1 of 7)
• Format of segment file (2 of 7)
• Format of segment file (3 of 7)
• Format of segment file (4 of 7)
• Format of segment file (5 of 7)
• Format of segment file (6 of 7)
• Format of segment file (7 of 7)
• Format of sequence file
• Format of trajectory file
• Format of free energy file
• Format of root mean square deviation file
• Format of property file

Format of MD files

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 (4 π εo in nm3)

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 (kJ nm2 mol-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 (kJ mol-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 (kJ mol-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 (kJ mol-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
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
I-2-1	a50	description of recorded property
For each recorded step one deck II
II-1-1	4(1pe12.5)	value of property

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