[gmx-users] energy minimization

[Mark Abraham]

Hi,

Typical force fields will have negative energies at minimize
configurations, but my guess is that your initial configuration has some
serious problem. Did you visualise the minimization start and end points?

Mark

On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji, <dmaji43 at gmail.com> wrote:

> Dear gromacs users,
>  I am doing energy minimization of a neat urea system. When I set emtol =
> 10 the following result is obtained  :
> Steepest Descents converged to machine precision in 33995 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  6.7910172e+04
> Maximum force     =  7.8070724e+01 on atom 353
> Norm of force     =  3.1714432e+00
> and average energy is
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Potential                   72421.6       2500    14229.1   -16147.4
>  (kJ/mol)
> And when I set emtol=100 the following result is obtained :
> Steepest Descents converged to Fmax < 100 in 12573 steps
> Potential Energy  =  7.1502609e+04
> Maximum force     =  8.5925835e+01 on atom 2713
> Norm of force     =  5.0333209e+00
> and average energy is
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Potential                   77654.4       3600    22408.3   -22901.6
>  (kJ/mol)
> In both cases the energy is well converged but not less than zero. Does
> only convergence of potential energy (not negative) guarantee the
> completion of EM process ? If so then what emtol value should  I use ?
> Any help will be highly appreciated. Thanks for your time.
> Best regards
> Dhrubajyoti Maji
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