[gmx-users] Minimization stops without reaching the requested precision Fmax < 1000

[Dallas Warren]

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 25 Jun 2019 at 04:03, Mahdi Bagherpoor <mehdi.bpour at gmail.com> wrote:
>
> Dear Gromacs Users,
>
> I am trying to add the tethrahedral zinc atom dummy model into CHARMM36
> force field in Gromacs. In my system, this dummy zinc interact with four
> Cystein residues (CYM).  The parameters of the zinc are available in CHARMM
> format, which I used to use it in NAMD package. After adding appropriate
> parameters, when I do energy minimization, I get this error:
> ========================
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your system).
> ...
> Steepest Descents converged to machine precision in 1045 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.5922652e+06
> Maximum force     =  3.2106902e+07 on atom 3526
> Norm of force     =  1.4857810e+05
>
> ============================
> Atom 3526 is dummy atom of zinc ion. The dummy parameters added in
> ffbonded.itp file are:
> ---------- ffbonded.itp
>
> ;zinc dummy model, bonds
>       HK       ZD     1   0.09000000    451872.00
>       HK       HK     1   0.14700000    451872.00
> ;zinc dummy model, angles
>       HK       ZD       HK     5   109.500000   460.240000   0.00000000
>     0.00
>       HK       HK       HK     5    60.000000   460.240000   0.00000000
>     0.00
>       HK       HK       ZD     5    35.250000   460.240000   0.00000000
>     0.00
> ;zinc dummy model, dihedrals
>       ZD       HK       HK       HK     9    35.300000     0.000000     2
>       HK       ZD       HK       HK     9   120.000000     0.000000     2
>       HK       HK       HK       HK     9    70.000000     0.000000     2
>
> ----------- ffnonbonded.itp
>
> ;zinc dummy model
>    ZD    30    61.380000    0.000  A  0.310000000000  0.00001
>    HK     1     1.008000    0.500  A  0.000000000000  0.00000
>
> =================================================
> In contrast to Gromacs, when I do minimization in NAMD, there is no such an
> error in minimization. I should mention that I am using single precision
> platform of Gromacs.
> I would appreciate if you could share me in case you have some ideas about
> this problem.
>
> Cheers,
> Mahdi
> --
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