[gmx-users] (no subject)

[Quyen V. Vu]

for what reasons you request the largest force in your system smaller than
such small value?

On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> Dear Gromacs users
> I am running a free energy calculation of the protein-ligand complex.
> During the energy minimization process, I am getting many jumps in steps as
> below:-
>
> Step           Time
>           10500    10500.00000
>
>    Energies (kJ/mol)
>            Bond Restraint Pot.          Angle    Proper Dih.  Improper Dih.
>     1.20860e+03    1.65864e+00    4.67218e+03    1.83350e+04    1.87873e+02
>           LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
>     6.81295e+03    7.12692e+04    3.37954e+05   -6.56537e+03   -2.70668e+06
>    Coul. recip.    Angle Rest.     Dih. Rest.      Potential Pres. DC (bar)
>     4.78029e+03    5.32468e+00    3.32764e+00   -2.26802e+06    0.00000e+00
>  Pressure (bar)    dVremain/dl       dEkin/dl      dVcoul/dl       dVvdw/dl
>    -2.69428e+04    0.00000e+00    0.00000e+00    2.78529e+03   -1.65404e+02
>  dVrestraint/dl   Constr. rmsd
>     0.00000e+00    2.71623e-06
>
>            Step           Time
>           10501    10501.00000
>
>            Step           Time
>           10502    10502.00000
>
>            Step           Time
>           10503    10503.00000
>
>            Step           Time
>           10504    10504.00000
>
>            Step           Time
>           10505    10505.00000
>
>            Step           Time
>           10506    10506.00000
>
>            Step           Time
>           10507    10507.00000
>
>            Step           Time
>           10508    10508.00000
>
>            Step           Time
>           10509    10509.00000
>
>            Step           Time
>           10510    10510.00000
>
>            Step           Time
>           10511    10511.00000
>
>
> 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 10512 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -2.2680185e+06
> Maximum force     =  6.3521606e+02 on atom 4653
> Norm of force     =  3.6713926e+00
>
> Should I use double precision for energy minimization?
> I need your suggestions,
>  please.
>
> Thanks
>
> Sadaf Rani
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