[gmx-users] question about the minimization

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Thu Oct 18 10:53:49 CEST 2012

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

I minimized it 30000 steps long but after step 20385 it stops with the

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,

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