AW: [gmx-users] question about the minimization

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Felix,
thank you for your answer.
So you think that a force of 3.2341940e+02 is okey? To work on?

I also tried to work on with a NVT run but then I got many many LINCS
warnings:

Step 1114, time 2.228 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3480   3482   30.3    0.1090   0.1092      0.1090

Step 1121, time 2.242 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000108, max 0.000561 (between atoms 2000 and 2001)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2002   2005   30.4    0.1090   0.1090      0.1090



And in the end there is the error:

Fatal error:
11 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposit
ion cell of their charge group in dimension x.


I looked it up on the GROMACS site and it was written there that such a
error is caused by a not well equilibrated system.

So I thought that the high force might be the reason.

What do you think?

Thanks again!!


> Hi Eva,
>
> The change in energy in every step became smaller than the machine
> precision can represent (as is stated in the output). In other words: your
> system is minimized to a very high degree.
> A value of 10 for the Fmax is very low for a system like yours, even with
> a pure protein in water system you probably wouldn't hit this value.
> Furthermore, 30.000 steps for a minimization seems pretty high to me.
>
> Cheers,
> Felix
>
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
> Gesendet: Donnerstag, 18. Oktober 2012 10:56
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] question about the minimization
>
> Hi everybody,
>
> I have a question about the minimization of my protein. For this
> minimization I fixed the backbone and the membrane atoms which around my
> protein.
>
> I minimized it 30000 steps long but after step 20385 it stops with the
> output:
>
> Steepest Descents converged to machine precision in 20385 steps, but did
> not reach the requested Fmax < 10.
> Potential Energy  = -8.8805600e+05
> Maximum force     =  3.2341940e+02 on atom 3050
> Norm of force     =  2.0930219e+00
>
> I do not see why it can not reach a lower force.
>
> I already looked at the structure with Pymol and there I saw that the atom
> 3050 is in a loop and do not interact with any other residue.
>
> My .mdp file looks like this:
>
> define                  = -DPOSRES
> integrator              = steep
> emtol                   = 10
> nsteps                  = 30000
> 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
>
> Do you see a reason why it can not reach a force lower than 10?
>
> Thank you,
>  Eva
>
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