[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 28/10/2011 2:30 AM, James Starlight wrote:
> That's energy ouptut from minimization with that parametries ( there 
> is also 1 step of steep minimization before that )
>
> integrator    = l-bfgs
> emtol        = 0.001
> emstep      = 0.001      ; Energy step size
> nsteps        = 5000000000          ; Maximum number of (minimization) 
> steps to perform
>
>
> ; Parameters describing how to find the neighbors of each atom and how 
> to calculate the interactions
> nstlist        = 1        ; Frequency to update the neighbor list and 
> long range forces
> ns_type        = grid        ; Method to determine neighbor list 
> (simple, grid)
> rlist        = 1.2        ; Cut-off for making neighbor list (short 
> range forces)
> coulombtype    = Shift
> rcoulomb        = 1.0
> rcoulomb_switch    = 0.7
> vdwtype         = Shift
> rvdw        = 1.0
> rvdw_switch     = 0.7
>
>
> Output:
>
> Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps
> Potential Energy  =  2.28946300988746e+03
> Maximum force     =  8.47298141911052e-04 on atom 100
> Norm of force     =  3.90346504086500e-04
>
> I'm not sure about the succses of that minimization due to the big Epot.
>
>

  You look like you are shuffling deck chairs on the Titanic. I 
suggested you actually go and visualize your input and output 
trajectories. Sadly that doesn't seem to have happened.

Mark
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