Gromacs Command-chapter1

Gromacs command very much, below I have recently used to summarize the first. The title also wrote this is just Chapter1, later will continue to write Chapter2 ... Wait a minute.

The following URL http://manual.gromacs.org/programs/byname.html all the Gromacs commands in alphabetical order, which is an official document. Part of my article may be taken from here, or from the content of the translated document.

• Pdb2gmx

PDB2GMX is a common command. Unfortunately I did not find an article on the Internet specifically to introduce this command, but I still think it is worthwhile to write a series specifically for the Gromacs command.

PDB2GMX is most commonly used to generate topology files. The following are its file-related directives:

-F: (input) structure file, gro PDB TPR is not common with g96 BRK ent ESP TPB TPA

-O: (output) structure file, gro pdb g96 BRK ent ESP

-P: (Output) topology file, top

-I: (output) Less commonly used, specify ITP files, the official document says include file for topology, generally refers to the Posre file.

-N: (output): Index file

-Q: Ignore it first

Some common directives:

-FF: Specifies the force field, and if you do not use this option, it will let you choose the force field.

-water: Designation water model, none, SPC, Spce, TIP3P, TIP4P, tip5p

-ignh:ignore hydrogen atoms that is in the coordinate file. Ignoring hydrogen atoms

• Editconf

Editconf can be used for conversion between files, and of course the greatest use is to build periodic boxes. The file directives are as follows:

-F: (input) structure file, gro,pdb, and other similar to PDB2GMX, the following no longer repeat

-O: (output) structure file, gro,pdb

-N:-bf:-mead:

Common commands are as follows:

-BT: Specify box type, Triclinic (three oblique), cubic (cubic), dodecahedron (12-face), octahedron (eight-face body)

-box:box vector Lengths (a,b,c) specify box vectors

-angles:angles between the box vectors (bc,ac,ab) vector angle

-d:distance between the solute and the box specifies the distance between the solute (protein) and the edge of the box, typically greater than 0.9nm

C: Specifies that the molecule is in the center of the box

-princ:orient molecule (s) along their principal axes molecule pointing spindle direction

-pbc:remove the periodicity (make molecule whole again) move out of periodicity, visual should not be used

-rvdw:default Van der Waals radius (in nm) if one can is found in the database or if no parameters is present in the The topology file specifies the VDW truncation distance, if no other place has this parameter.

• Grompp

The

GROMacs pre-processor preprocessor. Typically used to generate TPR files as input files for Mdrun. The official documentation is explained as follows:  reads a molecular topology file, checks the validity of the file, expands the topology from a molecular des Cription to an atomic description. The topology file contains information about molecule types and the number of molecules, the preprocessor copies each mole Cule as needed. There is no limitation on the number of molecule types. Bonds and Bond-angles can be converted to constraints, separately for hydrogens and heavy atoms. Then a coordinate file was read and velocities can be generated from a Maxwellian distribution if requested.  gmx g ROMPP  also reads parameters for  gmx mdrun   (eg. number of MD steps, time step, cut-off), and O Thers such as NEMD parameters, which is corrected so, and the net acceleration is zero. Eventually a binary file is produced this can serve as the sole input file for the MD program.

Approximate translation: Read and examine the topology file, extending from the molecular description to the atomic description, the topology file contains the molecular type, the number of molecules, the data required for GROMPP replication, there is no limit on the number and type of molecules, and the key and key angles are converted to limits (hydrogen atoms and heavy atoms are separated). Then read into the structure (GRO) file, generating the speed according to the Maxwell rate distribution (if necessary). Finally, the TPR file is claimed for Mdrun use.

File Instructions:

-F: (input) MDP file

-C: (input) structure file, Gro PDB

-P: (Input) topology file

-O: (output) TPR file

-ref: (input/output, optional) TRR file, full precision trace file

Other directives:

-v:be loud and noisy. Run-time output a lot of information

-maxwarn:number of allowed warnings during input processing. The number of warnings that are allowed for generate unstable systems

• Mdrun

Mdrun may be one of the most critical instructions, and the molecular dynamics run up on it.

GMX Mdrun is the main computational chemistry engine within GROMACS. Obviously, it performs Molecular dynamics simulations, but it can also perform Stochastic Dynamics, energy minimization, t  EST particle insertion or (re) calculation of energies. This is a sentence in the official document. It can be known that mdrun can do stochastic kinetic simulations, minimize energy, test particle insertion, calculate energy, and so on.

But in my contact with the tutorial, the general use of the command only two:

-v:be loud and noisy output run information, generally do not use the good

-deffnm:set the default filename for all file options. This command is very useful, because it directly defines the input of all file options, whether it is input or output, uniform use of-deffnm after the string, so that the input TPR file is defined by DEFFNM, and the output file name is also defined by DEFFNM.

For the time being these four commonly used commands, the other one has to write another Chapter2.

Gromacs Command-chapter1