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

Mon Feb 29 17:39:27 CET 2016

Dear Mark and Justin,

By removing the restraints (your suggestions) it appears to have worked!

Maximum force: 9.21098e-04
Writing Hessian...

This now matches the same force as my energy minimisation. Many thanks for
you help.

Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London

On 29/02/2016 14:46, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of mark.j.abraham at gmail.com> wrote:

>Hi,
>
>An earlier mdp file suggested you were using position restraints. There
>should be no need for this, nor any problem, but what happens without
>them?
>
>Mark
>
>On Mon, 29 Feb 2016 15:39 Nash, Anthony <a.nash at ucl.ac.uk> wrote:
>
>> Hi Justin,
>>
>> After some digging I had found that link and made some adjustments (as
>> presented in the later email).
>>
>> After a series of energy minimisations (including switching LINCS off,
>>and
>> dropping the energy step to a very small number), and with the final
>> command:
>> grompp_d -f cg.mdp -c modic_cg_3.gro -p system.top -o modic_cg_4 -t
>> modic_cg_3.trr
>>
>>
>> Polak-Ribiere Conjugate Gradients converged to Fmax < 0.001 in 6883
>>steps
>> Potential Energy  = -1.92681826422996e+03
>> Maximum force     =  8.54361662283108e-04 on atom 44
>> Norm of force     =  2.71110116926712e-04
>>
>>
>> However, when switching to integrator=nm, running grompp_d -f nma.mdp -c
>> modic_cg_4.gro -p system.top -o modic_nma -t modic_cg_4.trr, and then
>> mdrun_d, I get:
>>
>> Maximum force: 5.19179e+01
>> 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.
>>
>>
>>
>> I¹m still struggling to yield a maximum force during the integrator=nm
>> step, as presented from the earlier cg step. The .mdp files are
>>identical
>> with the exception of the integrator line.
>>
>> Thanks
>> Anthony
>>
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>>
>>
>>
>>
>> On 29/02/2016 12:49, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>on
>> behalf of Justin Lemkul"
>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
>> jalemkul at vt.edu> wrote:
>>
>> >
>> >
>> >On 2/29/16 3:41 AM, Nash, Anthony 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
>> >>
>> >
>> >Relying only on .gro format is insufficient precision to continue from
>> >minimization to NMA.  Make sure to pass the .trr to grompp -t.
>> >
>> >http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>> >
>> >-Justin
>> >
>> >--
>> >==================================================
>> >
>> >Justin A. Lemkul, Ph.D.
>> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >
>> >Department of Pharmaceutical Sciences
>> >School of Pharmacy
>> >Health Sciences Facility II, Room 629
>> >University of Maryland, Baltimore
>> >20 Penn St.
>> >Baltimore, MD 21201
>> >
>> >jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> >http://mackerell.umaryland.edu/~jalemkul
>> >
>> >==================================================
>> >--
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