AW: [gmx-users] question about the minimization

Rausch, Felix frausch at
Thu Oct 18 11:27:13 CEST 2012

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. 


-----Ursprüngliche Nachricht-----
Von: gmx-users-bounces at [mailto:gmx-users-bounces at] Im Auftrag von reisingere at
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users at
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

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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