[gmx-users] Energy Minimization of Alanin

Lara Bunte lara.bunte at yahoo.de
Wed Sep 19 12:04:47 CEST 2012


I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27.

I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. 

Next I want to run an energy minimization and I create this em.mdp file:

integrator         = steep         
emtol              = 1000.0      
emstep           = 0.01          
nsteps            = 5000          

nstlist             = 1               
rlist                = 0.7              
coulombtype   = PME    
rcoulomb        = 0.7         
vdw-type        = cut-off    
rvdw              = 0.7           
nstenergy      = 10

grompp works but I got this note:

NOTE 1 [file em.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. 

Thanks for help


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