[gmx-users] energy minimization

[David van der Spoel]

Dongsheng Zhang wrote:
> Hello, everyone,
> 
> I have a system with a nanotube and a polymer chain. First I did EM for
> the system in vacuum. After that, I added some water to  my system, and
> tried to do EM again. This time I got some large force on some atoms.
> The messages are as folllows:
> Step=    0, Dmax= 5.0e-03 nm, Epot= -4.89150e+06 Fmax= 6.50095e+04,
> atom= 2463
> Step=    1, Dmax= 5.0e-03 nm, Epot= -4.91505e+06 Fmax= 3.30822e+04,
> atom= 2463
> Step=    2, Dmax= 6.0e-03 nm, Epot= -4.96938e+06 Fmax= 1.72511e+04,
> atom= 2463
> Step=    3, Dmax= 7.2e-03 nm, Epot= -5.09757e+06 Fmax= 1.02066e+04,
> atom= 11109
> Step=    4, Dmax= 8.6e-03 nm, Epot= -5.39186e+06 Fmax= 8.89407e+03,
> atom= 11109
> Step=    5, Dmax= 1.0e-02 nm, Epot= -5.92594e+06 Fmax= 1.27715e+04,
> atom= 2464
> Step=    6, Dmax= 1.2e-02 nm, Epot= -6.59458e+06 Fmax= 3.53621e+04,
> atom= 10534
> Step=    7, Dmax= 1.5e-02 nm, Epot= -7.04583e+06 Fmax= 9.01766e+05,
> atom= 10534
> Step=    8, Dmax= 1.8e-02 nm, Epot= -7.12198e+06 Fmax= 6.09737e+07,
> atom= 2464
> Step=   14, Dmax= 6.7e-04 nm, Epot= -7.17427e+06 Fmax= 2.34996e+08,
> atom= 2463
> Step=   16, Dmax= 4.0e-04 nm, Epot= -7.20472e+06 Fmax= 3.88459e+08,
> atom= 2464
> Step=   18, Dmax= 2.4e-04 nm, Epot= -7.43615e+06 Fmax= 2.80954e+09,
> atom= 2463
> Step=   21, Dmax= 7.3e-05 nm, Epot= -1.05082e+07 Fmax= 2.44979e+11,
> atom= 2464
> Step=   25, Dmax= 1.1e-05 nm, Epot= -1.33633e+07 Fmax= 8.20246e+11,
> atom= 2463
> Step=   27, Dmax= 6.5e-06 nm, Epot= -1.60347e+07 Fmax= 1.66408e+12,
> atom= 2463
> Step=   29, Dmax= 3.9e-06 nm, Epot= -2.73531e+07 Fmax= 8.51628e+12,
> atom= 2463
> Step=   32, Dmax= 1.2e-06 nm, Epot= -3.69604e+08 Fmax= 2.72010e+15,
> atom= 2463
> Step=   33, Dmax= 1.4e-06 nm, Epot= -2.43314e+07 Fmax= 6.16803e+12,
> atom= 2463
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000

topology is wrong. check atom 2463

> 
> I believe something is wrong here. Could anyone give me a hand how to
> fix it? Thank you very much!
> 
> Have a nice weekend!
> 
> Dongsheng
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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