+------------------------------------------------------------------------------------------------------------+
| Parameters |
- +===================+===========================+=====+====+=========================================+=======+
- | interaction type | directive | # | f. | parameters | F. E. |
- | | | at. | tp | | |
- +-------------------+---------------------------+-----+----+-----------------------------------------+-------+
- | *mandatory* | ``defaults`` | non-bonded function type; |
- | | | combination rule\ |CRO|; |
- | | | generate pairs (no/yes); |
- | | | fudge LJ (); fudge QQ () |
+ +===================+===========================+=====+====+=================================================+
+ | interaction type | directive | # | f. | parameters |
+ | | | at. | tp | |
+ +-------------------+---------------------------+-----+----+-------------------------------------------------+
+ | *mandatory* | ``defaults`` | | non-bonded function type; |
+ | | | | combination rule\ |CRO|; |
+ | | | | generate pairs (no/yes); |
+ | | | | fudge LJ (); fudge QQ () |
+ +-------------------+---------------------------+----------+-------------------------------------------------+
+ | *mandatory* | ``atomtypes`` | | atom type; m (u); q (e); particle type; |
+ | | | | |VCR| ; |WCR| |
+ +-------------------+---------------------------+----------+-------------------------------------------------+
+ | | ``bondtypes`` | | (see |TREF|, directive ``bonds``) |
+ +-------------------+---------------------------+------------------------------------------------------------+
+ | | ``pairtypes`` | | (see |TREF|, directive ``pairs``) |
+ +-------------------+---------------------------+------------------------------------------------------------+
+ | | ``angletypes`` | | (see |TREF|, directive ``angles``) |
+-------------------+---------------------------+------------------------------------------------------------+
- | *mandatory* | ``atomtypes`` | atom type; m (u); q (e); particle type; |
- | | | |VCR| ; |WCR| |
+ | | ``dihedraltypes``\ |STAR| | | (see |TREF|, directive ``dihedrals``) |
+-------------------+---------------------------+------------------------------------------------------------+
- | | ``bondtypes`` | (see |TREF|, directive ``bonds``) |
- + + + +
- | | ``pairtypes`` | (see |TREF|, directive ``pairs``) |
- + + + +
- | | ``angletypes`` | (see |TREF|, directive ``angles``) |
- + + + +
- | | ``dihedraltypes``\ |STAR| | (see |TREF|, directive ``dihedrals``) |
- + + + +
- | | ``constrainttypes`` | (see |TREF|, directive ``constraints``) |
+ | | ``constrainttypes`` | | (see |TREF|, directive ``constraints``) |
+-------------------+---------------------------+-----+----+-------------------------------------------------+
| LJ | ``nonbond_params`` | 2 | 1 | |VCR| ; |WCR| |
- + + + + + +
+ +-------------------+---------------------------+-----+----+-------------------------------------------------+
| Buckingham | ``nonbond_params`` | 2 | 2 | |AKJM| ; |BNM|; |
| | | | | |C6LJ| (|KJN6|) |
+-------------------+---------------------------+-----+----+-------------------------------------------------+
.. table::
- +------------------------------------------------------------------------------------------------------------+
- | Molecule definition(s) |
- +===================+===========================+============================================================+
- | *mandatory* | ``moleculetype`` | molecule name; |NREX| |
+ +----------------------------------------------------------------------------------------------------+-------+
+ | Molecule definition(s) | F. E. |
+ +===================+===========================+=====+==============================================+=======+
+ | *mandatory* | ``moleculetype`` | | molecule name; |NREX| | |
+-------------------+---------------------------+-----+----------------------------------------------+-------+
| *mandatory* | ``atoms`` | 1 | atom type; residue number; | type |
| | | | residue name; atom name; | |
.. |NM4| replace:: (kJ mol\ :math:`^{-1}`\ nm\ :math:`^{-4}`
.. |DKJ| replace:: :math:`D` (kJ mol\ :math:`^{-1}`
.. |BETA| replace:: :math:`\beta` (nm\ :math:`^{-1}`
-.. |C23| replace:: :math:`C_{i=2,3}` (kJ mol\ :math:`^{-1}\ nm\ :math:`^{-i}`
+.. |C23| replace:: :math:`C_{i=2,3}` (kJ mol\ :math:`^{-1}`\ nm\ :math:`^{-i}`
.. |BMM| replace:: :math:`b_m`
.. |GE0| replace:: :math:`\geq 0`
.. |KO| replace:: :math:`k`
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| restricted dihedral | ``dihedrals`` | 4 | 10 | |PHI0| (deg); |KPHI| (|KJM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- | combined bending-torsion potential | ``dihedrals`` | 4 | 11 | |A0|, |A1|, |A2|, |A3|, |A4| (|KJM|) | |
+ | combined bending-torsion potential | ``dihedrals`` | 4 | 11 | |k_phi|, |A0|, |A1|, |A2|, |A3|, |A4|, (|KJM|) | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
| exclusions | ``exclusions`` | 1 | | one or more atom indices | |
+------------------------------------+----------------------------+------------+-----------+-------------------------------------------------------------------------+------------+
- Atoms in the same charge group must be listed consecutively
+- Bonded atom type name must contain at least one non-digit character.
+
- The file is parsed only once, which implies that no forward
references can be treated: items must be defined before they can be
used
the (non-)presence of parameters in the topology, x indicates that
the presence has no influence.
- +--------------------+---------------+---------------------------------+---------+
- | B-state atom types | parameters | parameters in bonded types | |
- + + +-----------------+---------------+ +
- | all identical to | on line | A atom types | B atom types | message |
- + +-------+-------+-------+---------+-------+-------+ +
- | A-state atom types | A | B | A | B | A | B | |
- +====================+=======+=======+=======+=========+=======+=======+=========+
- | | +AB | |NOT| | x | x | | | |
- | | +A | +B | x | x | | | |
- | yes | |NOT| | |NOT| | |NOT| | |NOT| | | | error |
- | | |NOT| | |NOT| | +AB | |NOT| | | | |
- | | |NOT| | |NOT| | +A | +B | | | |
- +--------------------+-------+-------+-------+---------+-------+-------+---------+
- | | +AB | |NOT| | x | x | x | x | warning |
- | | +A | +B | x | x | x | x | |
- | | |NOT| | |NOT| | |NOT| | |NOT| | x | x | error |
- | no | |NOT| | |NOT| | +AB | |NOT| | |NOT| | |NOT| | warning |
- | | |NOT| | |NOT| | +A | +B | |NOT| | |NOT| | warning |
- | | |NOT| | |NOT| | +A | x | +B | |NOT| | |
- | | |NOT| | |NOT| | +A | x | + | +B | |
- +--------------------+-------+-------+-------+---------+-------+-------+---------+
+ +--------------------+---------------+-----------------------------------+---------+
+ | B-state atom types | parameters | parameters in | parameters in | |
+ | | | bonded types | bonded types | expected|
+ | all identical to | on line | of A atoms | of B atoms | message |
+ | +-------+-------+-------+---------+-------+---------+ |
+ | A-state atom types | A | B | A | B | A | B | |
+ +====================+=======+=======+=======+=========+=======+=========+=========+
+ | yes | +AB | |NOT| | x | x | | | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | yes | +A | +B | x | x | | | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | yes | |NOT| | |NOT| | |NOT| | |NOT| | | | error |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | yes | |NOT| | |NOT| | +AB | |NOT| | | | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | yes | |NOT| | |NOT| | +A | +B | | | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | +AB | |NOT| | x | x | x | x | warning |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | +A | +B | x | x | x | x | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | |NOT| | |NOT| | |NOT| | |NOT| | x | x | error |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | |NOT| | |NOT| | +AB | |NOT| | |NOT| | |NOT| | warning |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | |NOT| | |NOT| | +A | +B | |NOT| | |NOT| | warning |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | |NOT| | |NOT| | +A | x | +B | |NOT| | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+
+ | no | |NOT| | |NOT| | +A | x | + | +B | |
+ +--------------------+-------+-------+-------+---------+-------+---------+---------+