[gmx-users] Normal mode analysis

[Valentin Gogonea]

Dear Gromacs users:

I am trying to get well optimized structures with Gromacs. I tried to 
optimize alanine (zwitterion). The max force wouldn't go less than 0.07 
and with this I still get 3 negative eigenvalues. I did 2000 steps but 
after about 230 steps the energy and the max force doesn't change 
anymore. Here are the parameters that I have used:

constraints         =  none
integrator          =  cg
nstcgsteep          =  50
dt                  =  0.002    ; ps !
nsteps              =  2000
nstlist             =  0
ns_type             =  simple
pbc                 =  no
rlist               =  0.0
rcoulomb            =  0.0
rvdw                =  0.0
coulombtype         =  cut-off
emtol               =  0.01
emstep              =  0.0001 (I tried different values for this 
starting from 0.001)

I would appreciate any comments and suggestions.

Valentin