Md energy minimization

User discussions
1

GROMACS version: 2019.1
GROMACS modification: No

Dear All

I am running simulations of a protein in water and on energy minimizations, I want to run both Steepest Descent and Conjugate Gradient methods. Firstly, I am very new to MD! I initially ran a separate steepest descent energy minimization step and that was succesful, but on trying to run the cg method I am getting the following error:

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

My .mdp file is as follows:
minim.mdp - input into grompp to generate em.tpr for energy minimization
; define = -DFLEXIBLE
integrator = cg ; Algorithm (cg = conjugate gradient minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nstcgsteep = 1000
nsteps = 5000 ; Maximum number of (minimization) steps to perform

Please assist me with how I can continue minimization after the steepest descent method with the cg method!

Thank you!

2

Since you have not specified the constraints keyword, it defaults to none, so the only constraints in the system are in water and require the use of define = -DFLEXIBLE, which you have commented out. If your constraints are failing, this means the system isn’t sufficiently minimized to proceed to CG minimization. Try using flexible water, then re-minimizing with whatever constraints are needed. If that fails, you probably can’t use CG, which is extremely sensitive. I never use it, honestly, due to the frequency of failure.