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

[Mark Abraham]

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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