[gmx-users] First Energy Minimization in a MD

Lara Bunte lara.bunte at yahoo.de
Sat May 12 22:25:14 CEST 2012


I read the mdp options more than once but I don't understand how to make a good em.mdp file for the first energy minimization, if you plug your molecule in a water box. In my tutorial is this example given.

integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10

1.) Is it possible to use this as a standard for all first energy minimization.

2.) Is the choose of parameters here dependent on the force field? I use a CHARMM27, do you think I should change something?

3.) What are the criteria to choose these parameters? As I said I read the mdp options, so I know what this Option above mean, but I don't know how to know that this are the right parameters? 

To say my question in other words: How do I know how the em.mdp file has to look like? 

Thanks for helping me.


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