# 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: (*C*cos(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 |