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 |