[gmx-users] putting step wise constraints in energy minimization

[Sadaf Rani]

Thank you, Justin,

I am still confused about constraints other than position restraints. As
mentioned
https://www.quora.com/q/gnvbdldrivyzzipw/Use-of-constraints-in-molecular-dynamics

Should I use constraints also for my system to converge better?
As I am doing energy minimization in two steps using steep emtol =100 and
constraints= all-bonds, which converges in 9116 steps

   Step           Time
           9115     9115.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    1.35583e+03    4.93367e+03    1.88532e+04    2.36071e+02    6.91634e+03
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
    7.12823e+04    3.37615e+05   -6.30626e+03   -2.68202e+06    5.72973e+03
      Potential Pres. DC (bar) Pressure (bar)
   -2.24140e+06    0.00000e+00   -2.56682e+04


Steepest Descents converged to Fmax < 100 in 9116 steps
Potential Energy  = -2.2414020e+06
Maximum force     =  9.0994179e+01 on atom 76219
Norm of force     =  3.3411843e+00

But the second minimization which I am doing in using steep integrator and
emtol= 10 and constraints=none shows that:-

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (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)

Steepest Descents converged to machine precision in 315 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -2.2420480e+06
Maximum force     =  2.9302316e+02 on atom 4379
Norm of force     =  3.5330992e+00
Finished mdrun on rank 0 Sun Feb 16 14:28:08 2020

How should I set the minimization energy of my system as it crashes after
some steps of nvt equilibration?

Thanks

Sadaf Rani
Ph.D. visiting student
Lancaster university
Uk