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

Michael Shirts mrshirts at gmail.com
Sat Jul 20 15:37:57 CEST 2013

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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