[gmx-users] Problem in energy minimization step

[Xuan Zhang]

Hi,

I am a newer to GROMACS. I want to simulate the CO2 + Water + Surfactant
system with GROMACS 2019.4. I generated the .pdb file with Packmol like
below. After the 50000 steps steep EM, I want to run the cg EM, but it
always had errors, One or more water molecules can not be settled.

Is it because of the box size in Packmol? I have checked the all the .itp,
.pdb files of surfactants, CO2 and H2O, and did not find error. Even I
removed the surfacants, just mixing CO2 and H2O, it still did not work.
However, when I exchange the surfactant type, sometimes it works.

Thank you for all your kind reply very much. Looking forward any advice.

Xuan

tolerance 2.0
filetype pdb
output mix.pdb

structure CO2.pdb
  number 5400
  inside box 0. 0. 0. 80. 80. 80.
end structure

structure C12.pdb
  number 30
  inside box 0. 0. 82. 80. 80. 122.
end structure

structure H2O.pdb
  number 12000
  inside box 0. 0. 130. 80. 80. 230.
end structure

structure C12.pdb
  number 30
  inside box 0. 0. 238. 80. 80. 278.
end structure

structure CO22.pdb
  number 5400
  inside box 0. 0. 280. 80. 80. 360.
end structure



step -1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

-------------------------------------------------------
Program:     gmx mdrun, version 2019.4
Source file: src/gromacs/mdrun/minimize.cpp (line 719)

Fatal error:
The coordinates could not be constrained. Minimizer 'cg' can not handle
constraint failures, use minimizer 'steep' before using 'cg'.







-- 
*Xuan Zhang*

zhangxuan7788 at gmail.com