Suggest me LAMMPS tutorial with commands exclusively for the protein dynamics. i have found out some document but that is not exclusively having the commands for the protein dynamics as like in GROMACS. Please suggest me some link or document.
Thank you....
If you download the LAMMPS source code, the "examples" directory within the LAMMPS folder has one called "peptide" which might be helpful to you. Among the files in this directory you should find "data.peptide" and "in.peptide". "data.peptide" is a LAMMPS data file which contains all the information about the atom positions, bond parameters, etc... In GROMACS terminology this file is kind of like the combination of a .gro and a .top file. The "in.peptide" file contains all of the parameters directing how to perform the MD run. In GROMACS terminology it is kind of like the .mdp file. If you play around with this example and read up about it in the manual (http://lammps.sandia.gov/doc/Manual.html), this should help you get started.
Sir Bryce Thurston ,
In data.peptide file , in "Atoms" section apart from following information :-
atom-No. , atom-ID , atom-type , q , x , y and z , there are three additional coloumn.
What information is written in those additional coloumns.
Thanks,
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