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

Nash, Anthony a.nash at ucl.ac.uk
Mon Feb 29 10:14:12 CET 2016 

Hi Tsjerk,

The two .mdp files are virtually identical (the only exception being what
defines one as a conjugate-gradient, and the other for normal mode
analysis):

CONJUGATE GRADIENT:
define = -DPOSRES
integrator      = cg
emtol           = 0.001
emstep          = 0.0002
nsteps          = 1000000
nstcgsteep      = 100
cutoff-scheme = verlet
nstlist         = 10
ns_type         = grid
rlist           = 1.4
coulombtype     = PME
rcoulomb        = 1.4
rvdw            = 1.4
pbc             = xyz


NORMAL MODE ANALYSIS
define = -DPOSRES
integrator = nm 
emtol = 0.001 
emstep = 0.0002 
nsteps = 1000000 
cutoff-scheme = verlet
nstlist = 10
ns_type = grid 
rlist = 1.4 
coulombtype = PME 
rcoulomb = 1.4 
rvdw = 1.4 
pbc = xyz 


The cg energy minimisation did NOT result in any warning about force not
converging. The result I got (I just re did it now) was:
Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6994 steps
Potential Energy  = -1.73087278108256e+03
Maximum force     =  9.97199385029354e-04 on atom 72
Norm of force     =  4.63373534634654e-04


But then when I run normal mode analysis (integrator=nm) I get:
Maximum force: 6.97334e+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.


My work flow:
grompp_d -f cg.mdp -c modic_en.gro -p system.top -o modic_cg
mdrun_d -deffnm modic_cg
grompp_d -f nma.mdp -c modic_cg.gro -p system.top -o modic_nma
mdrun_d -deffnm modic_nma






I sincerely hope I’m doing something wrong. That way it’ll be easier to
solve. 

Many thanks
Anthony


Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 08:03, "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 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
>> >>
>> >>
>> >> --
>> >> Gromacs Users mailing list
>> >>
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>> >>
>> >
>> >
>> >
>> >--
>> >Tsjerk A. Wassenaar, Ph.D.
>> >--
>> >Gromacs Users mailing list
>> >
>> >* Please search the archive at
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>> >posting!
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>
>
>
>-- 
>Tsjerk A. Wassenaar, Ph.D.
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
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