[gmx-users] EM problem

[David van der Spoel]

On Fri, 2002-11-08 at 15:35, sgaray at fbcb.unl.edu.ar wrote:
> Dear Gromacs user´s
> 
> My name is Sergio Garay  and I´m trying to minimize de E of a 
> bilayer of 72 stearic acid in a periodic boundary conditions. I´m 
> using ffG43a2x forcefield with and without position restraints in C of 
> carboxilic acids.
> Grompp preprocesator doesn´t give any warning but the EM doesn´t 
> work properly (log below). It doesn´t seems to work :
> 
> Stepsize too small (7.62939e-07 nm)Converged to machine 
> precision,
> but not to the requested precision (200)
> 
> Steepest Descents did not converge in 18 steps
>   Potential Energy  =  9.69202e+17
> Maximum force:          inf

energy is outrageous, check your starting structure...


> 
> 	M E G A - F L O P S   A C C O U N T I N G
> 
>    RF=Reaction-field  Free=Free Energy  SC=Softcore
>    T=Tabulated        S=Solvent         W=Water     WW=Water-Water
> 
>            Computing:      M-Number      M-Flop's  % Flop's
>                    LJ      3.521646    109.171026    15.4
>          LJ + Coulomb      0.006480      0.246240     0.0
>            Coulomb(T)      0.044208      1.812528     0.3
>       LJ + Coulomb(T)      0.132624      7.161696     1.0
>       Innerloop-Iatom      0.142542      1.425420     0.2
>      Spread Q Bspline      1.741824      3.483648     0.5
>      Gather F Bspline      1.741824     20.901888     3.0
>                3D-FFT     47.746584    381.972672    54.0
>             Solve PME      0.731808     46.835712     6.6
>              NS-Pairs      5.764806    121.060926    17.1
>          Reset In Box      0.027216      0.244944     0.0
>               Shift-X      0.027216      0.163296     0.0
>                CG-CoM      0.023328      0.676512     0.1
>                 Bonds      0.025920      1.114560     0.2
>                Angles      0.025920      4.224960     0.6
>               Propers      0.005184      1.187136     0.2
>             Impropers      0.001296      0.269568     0.0
>          RB-Dihedrals      0.019440      4.801680     0.7
>                Virial      0.000486      0.008748     0.0
>           Total                   706.76316   100.0
> 
>                NODE (s)   Real (s)      (%)
>        Time:     30.000     30.000    100.0
> 
> 
> When I tried to run a MD simulation starting with the EM_out.gro file 
> the system crashes (I guess, the system has very bad contact 
> between many atoms).
> 
> Also, I tryied a system with a stearic acid alone in vacuo and the EM 
> work fine (make some steps and change the potential Energy of the 
> system).
> 
> Could you give any advice?
> 
> Thank You.
> 
> Sergio 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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