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 fragment file
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 (1 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 \pi \epsilon_{o} in nm^{3}) |
Format of segment file (2 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 nm^{2} mol^{-1}) |
Format of segment file (3 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 (4 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(m\phi-\delta)) | ||
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 (5 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 (6 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 segment file (7 of 7)
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 sequence 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 trajectory file
Card | Format | Description |
For each step in (\lambda) 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 (\lambda) |
I-1-4 | f12.6 | step size of (\lambda) |
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 (\lambda) |
I-4-2 | e20.12 | average temperature at current (\lambda) |
I-4-3 | e20.12 | average exponent reverse perturbation energy at current (\lambda) |
I-4-4 | e20.12 | average exponent forward perturbation energy at current (\lambda) |
Format of free energy 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 root mean square deviation 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 |
Format of property file