# [gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Sun Oct 30 08:03:02 CET 2011

```Mark, hello!

I think that there is some error durins saving of my minimization data

As the result of the minimization I've obtained

(1)
Low-Memory BFGS Minimizer converged to machine precision in 3723 steps,
but did not reach the requested Fmax < 0.
Potential Energy  =  2.08789280994511e+03
Maximum force     =  3.01715687185776e-04 on atom 58
Norm of force     =  3.09301310600005e-05

So the Fmax is sufficient low

But when I've load this data for NMA I've obtained

(2)
Maximum force: 8.41270e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

So the Fmax is indeed very big for NMA but why it's not the same as in the
(1)?

This is my script for NMA wich indicate that I've load to NMA suitable data

# Steep
grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr

mdrun_d -v -deffnm minimizedS

grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o

# NMA
grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr

mdrun_d -v -deffnm fornma -mtx nm.mtx

Where is the error?

James

2011/10/28 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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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