[gmx-users] LINCS warning in md run

[Justin Lemkul]

On 9/12/12 3:39 PM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> my mdp file for the md run looks like this:
>
> define          = -DPOSRES
> integrator              = md
> dt                      = 0.001
> nsteps          = 5000
> nstxout         = 100
> nstvout         = 0
> nstfout         = 0
> nstlog          = 1000
> nstxtcout               = 500
> nstenergy               = 5
> energygrps              = Protein Non-Protein
> nstcalcenergy   = 5
> nstlist         = 10
> ns-type         = Grid
> pbc                     = xyz
> rlist           = 0.9
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw            = 0.9
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> gen_vel         = yes
> gen_temp                = 200.0
> gen_seed                = 9999
> constraints             = all-bonds
> tcoupl          = V-rescale
> tc-grps         = Protein  System_&_!Protein
> tau_t           = 0.1     0.1
> ref_t           = 298     298
> pcoupl          = no
> freezegrps = Protein_&_!TYP
> freezedim = Y Y Y
>
>
> I added a phosphate (TYP) to my protein and now want to do first a
> minimization (which I already did), then a short md run (for the case that
> I am in a local minima) and after that again a minimization.
> Since I only want to minimize the energy of the phosphate I freezed the
> rest of the protein (Protein_&_!TYP).
>
>
> Since on my cluster I am not allowed to run long jobs I had to divide the
> minimization run in several runs. The output of the last run was:
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7264606e+05
> Maximum force     =  1.6227990e+04 on atom 961
> Norm of force     =  1.2328220e+02
>
> gcq#192: "It's So Fast It's Slow" (F. Black)
>
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.7264606e+05
> Maximum force     =  1.6227990e+04 on atom 961
> Norm of force     =  1.2328220e+02
>
>
> After this minimization run I wanted to do the md run.
>
> My protein is a membrane protein with its surrounding membrane. I already
> did a minimization and md run with this protein but without the phosphate.
> The only difference to the time when everything worked fine is the
> phosphate.
>
> Does this help you somehow to see the failure?
>

Your minimization is insufficient.  You have a maximum force in excess of 16000 
on atom 961.  Such a large force explains the crash.  You should investigate 
what this atom is and what is pushing on it so hard.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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