[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

[Michael Shirts]

To follow up -- if I try to minimize again using -t, I get the same
low forces as in the minimization in the previous step.  So it appears
to be something with what do_nm is doing, not with errors in the
output structure.

On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts <mrshirts at gmail.com> wrote:
> When I minimize a structure, I can get down to the force max being <0.01
>
> Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
> Potential Energy  = -5.12340607768673e+03
> Maximum force     =  6.68907856457542e-03 on atom 3029
> Norm of force     =  2.19978176343026e-03
>
> kJ/nm.  However, when I try to perform a normal mode analysis, it
> complains that the maximum energy is >30 kJ/mn.
>
>
> Non-cutoff electrostatics used, forcing full Hessian format.
> Allocating Hessian memory...
>
> Maximum force: 3.91984e+01
> 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.
>
> I've restarted from the binary .trr output (-t option) , and I'm using
> double precision. Any suggestions as to why the force max is not the
> asme on restarting?  Only difference is going from l-bfgs to nm.
>
> I've seen some older comments on this, but no resolution and nothing recent.