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

[Justin Lemkul]

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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