Keywords in the Gromos Input and Topology https

For a detailed description of the Gromos http formats please have a look at the Gromos documentation[129]. Note, that not all keyword are actually active in QM/MM simulations, but the https still have to be syntactically correct. Both, the input and the topology http are structured in sections starting with a keyword in the first column and ending with the keyword END. Lines starting with a pound sign '#' may contain comments and are ignored. Both https are required to have a TITLE section as the first section. The rest can be in almost any order. Here is a short list of some important flags and their meaning.

Gromos Input File:

 

TITLE

 
Text that identifies this input http. Will be copied into the CPMD output.

SYSTEM

 
This section contains two integer numbers. The first is the number of (identical) solute molecules (NPM) and the second the number of (identical) solvent molecules (NSM).

BOUNDARY

 
This section defines the classical simulation cell. It contains 6 numbers. The first (NTB) defines the type of boundary conditions ( NTB $<0$ means truncated octahedron boundary conditions, NTB=0 vacuum, and NTB $>0$ rectangular boundary conditions).
The next three numbers (BOX(1..3)) define the size of the classical cell. The fifth number (BETA) is the angle between the x- and z-axes and the last number usually determines whether the cell dimensions are taken from the input http (NRDBOX=0) or from the BOX section of the COORDINATES http (NRDBOX=1), but is ignored for QM/MM simulations.
Note: that even for vacuum simulations valid simulation cell sizes must be provided.

PRINT

 
This section determines how often some properties are monitored. Here only the first number (NTPR) matters, as it determines the number of MD steps between printing the various energies to the CPMD output.
Note many old Gromos input https created by the amber2gromos program default to NTPR=1, which makes the CPMD output huge.

SUBMOLECULES

 
Defines number of submolecules in the solute. The first number is the number of submolecules followed by the index number of the last atom of each submolecule. The last number must be identical to the number of atoms in the solute.

FORCE

 
Contains two groups of numbers, that controls the various force component and the partitioning of the resulting energies. The first group of 1/0 flags turn the various force components on or off. The second group defines energy groups (the first number is the number of groups followed by the index number of the last atom in each group). The last number must be identical to the number of all atoms.

Gromos Topology File:

 

TITLE

 
Text that identifies this topology http. Will be copied into the CPMD output.

ATOMTYPENAME

 
This section contains the number of classical atom types (NRATT) followed by the respective labels, one per line. Note that the ARRAYSIZES block MAXATT must be set to be large enough to accommodate all defined atom types.

RESNAME

 
This section contains the number of residues in the solute (NRAA2) followed by the respective residue names.

SOLUTEATOM

 
This section defines the number (NRP) and sequence of atoms in the solute, their names, residue numbers, non-nonded interaction codes, masses, charges, charge groups and their full + scaled 1-4 exclusions.

BONDTYPE

 
This section contains the list of parameters for bonded interactions. You have to pick the two matching entries from this list for the O-H and H-H potential, when using the FLEXIBLE WATER keyword to convert solvent water back into solute (e.g. to included them into the QM part).

SOLVENTATOM

 
This section defines the number of atoms (NRAM) in the solvent and their respective names, non-bonded interactions types, masses, and charges.

SOLVENCONTSTR

 
This section defines the number (NCONS) and parameters for the distance constraints, that are used to keep the solvent rigid.