I wanted to perform a molecular dynamics simulation for a kinase and wanted to know how to generate mdp files for adding ions after solvation ? I could successfully generate the topol.top files and other files but I wanted to know how to generate the mdp files for next step of ionization useing gmx grompp.
Here's an example mdp file: http://www.mdtutorials.com/gmx/lysozyme/Files/ions.mdp
You can edit this as per requirements.
Joydeep Roy Hi
It is very easy to create the ions.mdp file. You will get a by default ion.mdp file on http://www.mdtutorials.com/gmx/complex/04_ions.html that file editable as per your need.
Just simply click on below link
http://www.mdtutorials.com/gmx/complex/Files/ions.mdp
just copy the whole text and paste into the notepad(windows)/text(linux) editor and save the file by rename ions.mdp.txt (just remove ".txt"----for windows)/ions.mdp their file name
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