[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?
mrshirts at gmail.com
Sat Jul 20 15:43:09 CEST 2013
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
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.
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