Hi i just started molecular dynamic simulation with gromacs . can anyone help me for 15-25 nano second analysis. shear with me script files and manual for simulation on Ubuntu if it is possible.
There is no simple recipe for analysis. What you measure depends on what the system is and what your scientific questions are.
There is no simple recipe for analysis. What you measure depends on what the system is and what your scientific questions are.
i am trying to learn protein ligand complex simulation with gromacs simulation, following gromacs tutorial. i successfully generated all topology file, newbox.gro and, topology.top files next is add ions but it requires em.mdp file as input file, i dont know how to get this one.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
thanks i tried this one but this gives an error:
Fatal error:
Atoms in the .top are not numbered consecutively from 1
i am attaching my topology.top file here
You mention 1 molecule of "l" in your system...Is it an ion? I can not find it defined ... maybe that generate your mistake.
- Badges
- Science topic