Gromacs file-chapter1

Gromacs file is very much, this is the official document address: http://manual.gromacs.org/online/files.html.

Part of this article is from the following URL https://zhuanlan.zhihu.com/p/27279508

I would like to make a brief introduction, the internal structure of the document that involves PDB,GRO,MDP is not introduced here, but opens separately.

Parameter file:

MDP: A separate explanation for other articles

M2P: Temporarily useless

Structure file:

Gro:gromacs format

g96:gromacs-96 format

Pdb:protein Databank

General structure files: Gro g96 pdb TPR TPB TPA

Topology file:

Top: System Topology File

Itp:include topology is a sub-topology file contained by the main topology file (. top), which typically contains the type of a particular molecule. The Yu Site topology file distinguishes between having it not referencing other force field files and including topological bytes such as [System],[molecule].

RTP: Residual base topology file. This file contains the field information of the common residues, including the atoms contained in the residues, key types, etc. When using PDB2GMX to process PDB files, the program looks for the corresponding residual field information in the RTP file according to the PDB file information.

NDX: Atomic index file (. ndx). The file contains an atomic ordinal number, when using the MAKE_NDX program to generate an index file, you can define different atomic groups, each group name is the number of each atom contained in the group.

Run the input file:

TPR: System topology, parameters, coordinates, speed (binary file, portable files Portable)

TPA: System topology, parameters, coordinates, speed (ASCII)

TPB: System topology, parameters, coordinates, speed (ascii,binary)

General Run input file: TPR TPA TPB

Trace file:

Tng:any kind of data (compressed, portable, any precision)

Trj:x, V and f (binary, full precision)

Trr:x, V and f (binary, full precision, portable)

Xtc:x only (compressed, portable, any precision)

Gro:x and V (ASCII, any precision)

G96:x only (ASCII, fixed high precision)

Pdb:x only (ASCII, reduced precision)

Formats for full-precision data: TNG, trr or trj

Generic trajectory formats: TNG, XTC, trr, trj, Gro, g96, PDB

Energy files:

Ene:energies, temperature, pressure, box size, density and virials (binary)

Enr:energies, temperature, pressure, box size, density and virials (binary, portable)

The System Energy file (ENERGY,.EDR) of the analog output. The file records the various interaction energies of the energy groups defined in the analog input file.

Other files:

LOG: Journal file

CPT: This file is an analog breakpoint file (check point,.cpt). This file is generated at a fixed time interval of the simulation process, saving all the information of the simulation system. Part of the file can be found in the energy file (. EDR), which can be found in a double-precision trace file (. trr). If the simulation is unfortunate because of external conditions (such as a power outage, the simulator loses his temper to the computer, etc.), you can use the file to start the simulation at the breakpoint again to save the simulation time. You can also rely on the breakpoint file to start and extend the simulation (see TPBCONV).

Gromacs file-chapter1