[gmx-users] LINCS warning in md run

[Justin Lemkul]

On 9/18/12 8:58 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Okey,
>   now I tried it without any fixed residues. But still the energy after the
> minimization is not very low and I still get the LINCS warnings.
>
> The mdp file I use for the minimization looks like this:
>
> define                  = -DPOSRES

Restraints during minimization generally restrict motion in the same way that 
freezing does.  Again, this is a potential barrier to sufficient minimization.

> integrator              = steep
> emtol                   = 10
> nsteps                  = 1500
> nstenergy               = 1
> energygrps              = System
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw                    = 0.9
> rlist                   = 0.9
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> pbc                     = xyz
>
>
> the 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  Non-Protein
> tau_t           = 0.1     0.1
> ref_t           = 298     298
> pcoupl          = no
>
>
>
> The output of the minimization run is:
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.9280412e+05
> Maximum force     =  1.0772942e+04 on atom 979
> Norm of force     =  9.6685356e+01
>

Note that this outcome is even worse than before.  The maximum force is now over 
10,000.

>
>
>
> The output of the MD run is:
>
> Step 1031, time 1.031 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001431, max 0.010707 (between atoms 976 and 979)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      976    979   81.6    0.1272   0.0970      0.0960
>
>

As you should expect.  If you can't get a reasonable minimization, the MD will 
always crash.

>
> The atom 979 is the hydrogen atom on the phosphate. There has to be one
> hydrogen atoms because it is protonated once. The other atom 976 is the
> oxygen atom where the hydrogen atom is bound to.
> The bounding parameters for this kind of binding were already there. I
> didn't add them.
>
> I already did it for another phosphorylation on another position in this
> structure. And here I also got many LINCS errors. And again the problem is
> the connection between the hydrogen atom and the oxygen atom.
>
> But I do not understand why.

Remove all restraints/freezing/whatever in the .mdp file and try the EM again. 
If it still does not converge to a reasonable value, then there are two 
potential problems:

1. The topology is flawed and thus the structure cannot be run stably
2. The structure cannot accommodate phosphate in this location and due to 
unresolvable clashes, the runs fail

-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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