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

Mon Feb 29 09:03:18 CET 2016

Hi Anthony,

You can paste your exact workflow commands and mdp files, but that would be
to just check whether you overlooked something. If you assert that the mdp
files are the same, except for the integrator and you really did use the
final minimized structure as input for the nm run, then it seems
something's fishy. You could make a run input file with integrator=cg and
integrator=nm and compare the two tpr files to see if something was changed
implicitly.

Cheers,

Tsjerk

On Mon, Feb 29, 2016 at 6:57 AM, Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.