[gmx-users] energy minimization error

[faride badalkhani]

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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