Output File Structure
- • conf.pdb : DNA PDB file after energy minimization and MD simulation by GROMACS. Files with the pdb extension are molecular structure files in the protein databank file format. The protein databank file format describes the positions of atoms in a molecular structure. Coordinates are read from the ATOM and HETATM records, until the file ends or an ENDMDL record is encountered. GROMACS programs can read and write a simulation box in the CRYST1 entry.
- • topol.top : Topology file of DNA. GROMACS must know on which atoms and combinations of atoms the various contributions to the potential functions must act. It must also know what parameters must be applied to the various functions. All this is described in the topology file top, which lists the constant attributes of each atom.
• *.itp : The itp file stands for include topology. These files are included in topology files. It contains properties of atoms, bonding informaion, and position restraints
• md.* : Output file of molecular dynamics conducted by md.tpr.
• mini.* : Output file of energy minimizing conducted by mini.tpr.
- .gro : The gro file contain a molecular structure in Gromos87 format. gro files can be used as trajectory by simply concatenating files.
- .tpr : The tpr file stands for portable binary run input file. This file contains the starting structure of the simulation, the molecular topology and all the simulation parameters.
- .mdp : The mdp file contains simulation parameters and is utilized for the generation of the tpr file.
- .cpt : The cpt file stands for portable checkpoint file. The entire simulation state, including extended thermostat/barostat variables, random number states, and NMR time averaged data, is stored in the checkpoint file.
- .log : The log file is generated by some GROMACS programs and are usually in human-readable format.
- .edr : The edr file stands for portable energy file. The energies are stored using the xdr protocol.
• *.ff : The Force-Field file that this application uses. One of them was uesd to simulation according your choice. A force field is built up from two distinct components:
- The set of equations (called the potential functions) used to generate the potential energies and their derivatives, the forces. These are described in detail in the previous chapter.
- The parameters used in this set of equations. These are not given in this manual, but in the data files corresponding to GROMACS distribution.
Within one set of equations, various sets of parameters can be used. Care must be taken that the combination of equations and parameters form a consistent set.
• Input DNA sequence. A, T, G, and C are only allowed
• The stability of DNA is maximized when the number of sequences aligns with a multiple of 10.5, owing to its double helix structure. Hence, it is recommanded to utilize either 21 or 42.