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

Michael Shirts mrshirts at gmail.com
Sat Jul 20 15:58:05 CEST 2013

Problem partly addressed.  If I run normal modes in -nt 1, then I get
the same force as after the minimization.

I'll file a redmine.

On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts <mrshirts at gmail.com> wrote:
> 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.

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