[gmx-users] Minimising forces for vibrational normal mode analysis

[Nash, Anthony]

Hi Tsjerk,

Compiled in double precision. I’ve alternated between steepest and
conjugate gradient. I am slightly confused over why the energy
minimisation reports a "Maximum force     =  3.72351263315387e-05 on atom
34” only then for integrator=nm to report "Maximum force: 6.02183e+02”,
which will presumably return in an imaginary frequency (I haven’t tried -
yet even if it didn’t I would be suspicious given the earlier warning).

Thanks
Anthony 


Dr Anthony Nash
Department of Chemistry
University College London





On 28/02/2016 22:04, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Tsjerk Wassenaar"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
tsjerkw at gmail.com> wrote:

>Hi Anthony,
>
>You do not state whether Gromacs was compiled in double precision or not.
>It should be for this stuff. In addition, you can try another minimization
>method. Sometimes alternating minimization methods may help to reach a
>proper minimum.
>
>Cheers,
>
>Tsjerk
>
>On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>> Hi all,
>>
>> I would like to pull out the vibrational normal modes using gromacs
>>over a
>> customised fragment to compare back with the original QM frequency
>> analysis.
>>
>> I¹ve performed an integrator=cg over my structure, and monitored the
>> potential energy which converges. The forces also converge beneath the
>> requested precision (as 0.0001, as per gromacs manual). The message:
>>
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>> Polak-Ribiere Conjugate Gradients:
>>    Tolerance (Fmax)   =  1.00000e-04
>>    Number of steps    =      1000000
>>    F-max             =  7.35939e+03 on atom 79
>>    F-Norm            =  1.68505e+03
>>
>> writing lowest energy coordinates.
>>
>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 8350
>>steps
>> Potential Energy  = -1.67001242395943e+03
>> Maximum force     =  3.72351263315387e-05 on atom 34
>> Norm of force     =  1.20696019277311e-05
>>
>>
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>>
>> When I then come to run integrator=nm I get a maximum force at odds with
>> the maximum force reported at the final stage of my energy minimisation:
>>
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>> Maximum force: 6.02183e+02
>> The force is probably not small enough to ensure that you are at a
>>minimum.
>> Be aware that negative eigenvalues may occur
>> when the resulting matrix is diagonalized.
>>
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>>
>>
>> When I decrease the force tolerance in the integrator=cg energy
>> minimisation to 0.00001 I end up with a poorer force convergence
>>(although
>> the potential energy is almost the same, but also the integrator=nm will
>> result in the same measure of maximum force):
>>
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>> Polak-Ribiere Conjugate Gradients:
>>    Tolerance (Fmax)   =  1.00000e-05
>>    Number of steps    =      1000000
>>    F-max             =  7.35939e+03 on atom 79
>>    F-Norm            =  1.68505e+03
>>
>> Energy minimization has stopped, but the forces have not converged to
>>the
>> requested precision Fmax < 1e-05 (which may not be possible for your
>> system).
>> It stopped because the algorithm tried to make a new step whose size was
>> too
>> small, or there was no change in the energy since last step. Either
>>way, we
>> regard the minimization as converged to within the available machine
>> precision, given your starting configuration and EM parameters.
>>
>> writing lowest energy coordinates.
>>
>> Polak-Ribiere Conjugate Gradients converged to machine precision in 9839
>> steps,
>> but did not reach the requested Fmax < 1e-05.
>> Potential Energy  = -1.67001242392665e+03
>> Maximum force     =  1.63690887039393e-03 on atom 34
>> Norm of force     =  3.34598700357485e-04
>> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>>
>>
>>
>> I don¹t want to end up with any imaginary values when I diagonalise the
>> hessian, any idea how to improve this performance? I am concerned with
>>the
>> output "Energy minimization has stopped, but the forces have not
>>converged
>> to the requested precision Fmax < 1e-05 (which may not be possible for
>> your system).² a a possible indication to the computational limitation
>>of
>> my machine.
>>
>> Many thanks
>> Anthony
>>
>>
>> --
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>
>
>
>-- 
>Tsjerk A. Wassenaar, Ph.D.
>-- 
>Gromacs Users mailing list
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