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

The tutorial provides a suitable .mdp file in step 4.

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.

Hi

Regarding the  error "Fatal error:

Atoms in the .top are not numbered consecutively from 1"

it seems that in ligand protein .gro file . both protein and ligand should be generated by same FF , 

According to the tutorial (Dr. Justin L. "http://www.bevanlab.biochem.vt.edu/...x-tutorials/complex/01_pdb2gmx.html") the ligand is numbered 1LIG and the atoms are also numbered from 1 to n right after the protein .However, maybe the second column (atom names ) should be in same format. Regards