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

Nash, Anthony a.nash at ucl.ac.uk
Mon Feb 29 11:11:19 CET 2016 

I noticed that I hadn’t included LINCS parameters in the mdp file. I have
included and currently running using:

continuation = no
constraints     = all-bonds             ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter      = 2                         ; accuracy of LINCS
lincs_order     = 8                         ; also related to accuracy


I upped lincs_iter from 1 to 2, and lincs_order from 4 to 8. The manual
says this is ideal for increasing accuracy during energy minimisation.

After performing this run I’m now getting forces beyond Fmax and I’ve
reached the maximum number of steps.
Potential Energy  = -1.71320900832000e+03
Maximum force     =  1.80888456004520e+01 on atom 13
Norm of force     =  7.70125465905422e+00


Prior to including LINCS, the system was finishing within 1000 steps, so I
feel as though I’m heading down the right paths in trying to get these
forces down first now that I’ve included lincs.




Dr Anthony Nash
Department of Chemistry
University College London





On 29/02/2016 08:41, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Nash, Anthony"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
a.nash at ucl.ac.uk> wrote:

>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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>>
>>
>>
>>-- 
>>Tsjerk A. Wassenaar, Ph.D.
>>-- 
>>Gromacs Users mailing list
>>
>>* Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>posting!
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>
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