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

[Justin Lemkul]

On 2/16/20 9:37 AM, Sadaf Rani wrote:
> 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

Constraints should be employed in a manner consistent with the force 
field parametrization strategy. Some force fields constrain all bonds 
(GROMOS) while others constrain only bonds to H (all the others). Use 
what the force field requires. If you don't use the appropriate 
constraints during minimization, your initial state may fail due to 
incompatibility of the geometry with the chosen (necessary) constraints.

>     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?

There are many reasons for systems to crash; see 
http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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