[gmx-users] Energy minimization problem for POPE/POPG soluted bilayer taken from M. Karttunen website

daniel depope nevjernik at gmail.com
Thu Sep 19 13:01:40 CEST 2019

Dear users

I tried energy minimization of POPE/POPG bilayer from
http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces
have not converged to requested precision (output shown below). I used
Gromacs version 2019.2 .

My colleague also used this bilayer before with earlier version of Gromacs
(don't know which one, sorry, few years ago), and everything works fine.

I tried a few different bilayers constructed from this one, and noticed
that different atoms causes a problem (Fmax on it) but each time it's about
H6 atom in some DPO molecule. I checked, and there is no steric clashes
with periodic images or solution molecules.

Any suggestions what could be wrong?


Below are tipical gromacs output and mdp file:

Gromacs output:
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot= -3.45240e+05 Fmax= 6.29238e+03, atom=
Step=    1, Dmax= 1.0e-02 nm, Epot= -3.51348e+05 Fmax= 3.62527e+03, atom=
Step=    2, Dmax= 1.2e-02 nm, Epot= -3.55043e+05 Fmax= 1.07906e+04, atom=
Step=    3, Dmax= 1.4e-02 nm, Epot= -3.58399e+05 Fmax= 6.04668e+03, atom=
Step=    4, Dmax= 1.7e-02 nm, Epot= -3.58764e+05 Fmax= 1.66084e+04, atom=
Step=    5, Dmax= 2.1e-02 nm, Epot= -3.62991e+05 Fmax= 3.55133e+04, atom=
Step=    6, Dmax= 2.5e-02 nm, Epot= -3.66326e+05 Fmax= 3.14946e+05, atom=
Step=    7, Dmax= 3.0e-02 nm, Epot= -3.66358e+05 Fmax= 6.27472e+04, atom=
Step=    8, Dmax= 3.6e-02 nm, Epot= -3.70907e+05 Fmax= 7.76457e+05, atom=
Step=   10, Dmax= 2.1e-02 nm, Epot= -3.71321e+05 Fmax= 1.24828e+06, atom=
Step=   14, Dmax= 3.2e-03 nm, Epot= -4.38973e+05 Fmax= 7.26301e+07, atom=
Step=   18, Dmax= 4.8e-04 nm, Epot= -4.39005e+05 Fmax= 1.17286e+08, atom=
Step=   28, Dmax= 1.1e-06 nm, Epot= -4.39005e+05 Fmax= 1.16818e+08, atom=
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.
integrator = steep
emtol = 1000.0
emstep      = 0.01
nsteps = 50000
nstlist = 1    ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
pbc    = xyz

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