AW: [gmx-users] question about the minimization
frausch at ipb-halle.de
Thu Oct 18 11:27:13 CEST 2012
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.
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users at gromacs.org
Betreff: [gmx-users] question about the minimization
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?
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