[gmx-users] Energy minimization error

[Mark Abraham]

Hi,

What some visualization program shows about bonds doesn't mean anything -
it has not parsed your topology. You have no option but to look at the .top
produced and reason about what it shows, but yours is very complex. I
strongly recommend starting with something simpler than a multiply branched
dendrimer. Join two units with a specbond, inspect the .top so that you
know it has what you think it has, and get that to EM and simulation
stably. Then you can get more complex.

Mark

On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani <farideh.khamseh at gmail.com>
wrote:

> Dear gromacs users,
>
> As I said before I faced with the minimization error, so I changed
> coordinates of atoms in pdb file, but the problem is the same. the only
> thing that changes in every run is atom number. I modified pdb for many
> times.
>
> Steepest Descents converged to Fmax < 1000 in 530 steps
> Potential Energy  = -5.5180181e+05
> Maximum force     =  7.4496063e+02 on atom 501
> Norm of force     =  3.8248455e+01
>
>
> Moreover gro structure was completely messed up when was visualized in vmd.
> you can see the picture of my structure in below dropbox link:
>
> https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
>
> and this is the pdb file dropbox link:
>
> https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
>
>
> I used cg algorithm after steep for minimization, too. But it did not work.
> is there any way to solve this problem?
>
> any help is appreciated.
>
> On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Look at atom 380 and see why the forces might be high.
> >
> > Mark
> >
> > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > farideh.khamseh at gmail.com>
> > wrote:
> >
> > > Thank you for your great help on specbond.dat file. I defined it and I
> > > could go ahead until Energy minimization step. I have used this
> minim.mdp
> > > file
> > >
> > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > ; Parameters describing what to do, when to stop and what to save
> > > integrator    = steep        ; Algorithm (steep = steepest descent
> > > minimization)
> > > emtol          = 1000.0      ; Stop minimization when the maximum
> force <
> > > 1000.0 kJ/mol/nm
> > > emstep       = 0.01          ; Energy step size
> > > nsteps        = 50000          ; Maximum number of (minimization) steps
> > to
> > > perform
> > >
> > > ; Parameters describing how to find the neighbors of each atom and how
> to
> > > calculate the interactions
> > > nstlist              = 1        ; Frequency to update the neighbor list
> > and
> > > long range forces
> > > ns_type           = grid        ; Method to determine neighbor list
> > > (simple, grid)
> > > rlist                 = 1.0        ; Cut-off for making neighbor list
> > > (short range forces)
> > > coulombtype    = PME        ; Treatment of long range electrostatic
> > > interactions
> > > rcoulomb         = 1.0        ; Short-range electrostatic cut-off
> > > rvdw               = 1.0        ; Short-range Van der Waals cut-off
> > > pbc                 = xyz         ; Periodic Boundary Conditions
> (yes/no)
> > >
> > > But when I run mdrun -v -deffnm em command, I get this error:
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (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 90 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -2.3956744e+05
> > > Maximum force     =  1.5824519e+05 on atom 380
> > > Norm of force     =  1.7695243e+03
> > >
> > > gcq#187: "Been There, Done It" (Beavis and Butthead)
> > >
> > > farideh at farideh-P61A-D3:~/FARIDEH$
> > >
> > > I changed the emtol, emstep, and nsteps for a few times. However, I
> > > couldn't resolve this problem. Could you tell me if there is something
> > > wrong with the minim.mdp file?
> > >
> > > You can see all the files via:
> > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> > >
> > > Truly yours,
> > > Farideh
> > > --
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