[gmx-users] energy minimization error

Fri Oct 23 19:05:30 CEST 2015

Hi,

pdb2gmx and grompp are pretty talkative about things like missing
parameters and bonds - go back and read what they had to say, and
particularly what pdb2gmx thought about your specbonds.

Mark

On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani <farideh.khamseh at gmail.com>
wrote:

> Hi,
>
> Thanks a lot for your time and patience. This time, I chose a very simple
> structure and then inspected the generated topology. The interesting point
> was that, there were some missing interactions. When I inspected them. I
> found that I had defined those interactions in ffbonded.itp file, but
> pdb2gmx has not assigned those definitions to these interactions. However,
> I added the appropriate gb_, ga_, or gd_ manually, and then performed the
> MD simulations and received an error as follows:
>
> Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom=
> 46
> Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom=
> 44
> Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom=
> 46
> Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom=
> 44
> Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom=
> 46
> Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom=
> 44
> Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom=
> 46
> Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom=
> 44
> Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom=
> 46
> Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom=
> 44
> Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom=
> 46
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 100 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 236 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -8.9157188e+04
> Maximum force     =  1.7089320e+05 on atom 44
> Norm of force     =  3.3110510e+03
>
> gcq#220: "Let's Go Hang Out In a Mall" (LIVE)
>
> farideh at farideh-P61A-D3:~/multiple/G0$
>
> you can access all the files via the following link:
> https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0
>
> Truly yours,
> Farideh
>
> On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Did you inspect your topology like I suggested? You need to know that
> there
> > are bonds exactly where you intend them, before doing any calculations
> with
> > them.
> >
> > Mark
> >
> > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> > farideh.khamseh at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I am trying to simulate a hyper-branched polymer (a dendrimer) in
> water.
> > > But, every time the system blows up at energy minimization step.
> > Therefore,
> > > according to what Mark had recommended I decided to start with a much
> > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I
> had
> > > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > > residue by residue. After that, I started simulation procedure and
> > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face
> any
> > > errors in energy minimization step, and the potential energy - EM step
> > plot
> > > was reasonable. But, when I loaded em.gro file in VMD, the structure
> was
> > > completely messed up as in G3 dendrimer. This time I continued the MD
> > > simulation until production MD, and there was no error. However, the
> > system
> > > is blown up. You can access all the simulation files, pdb structure,
> and
> > > the photos of G1 structure before and after EM step via:
> > >
> > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> > >
> > > Since I am a beginner in this area, I do not know what is the solution
> > for
> > > this problem.
> > > Do you think errors that occur during the G3 simulation are relevant to
> > the
> > > initial structure?
> > > any suggestion or recommendation is appreciated.
> > >
> > > Thanks in advance
> > > Farideh
> > > --
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