Re: [gmx-users] a problem in the energy minimization.the

[Florian Haberl]

Hi,

read the wiki or search the mailing list archive
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision


On Tuesday, 14. August 2007 11:28, [EMAIL PROTECTED] wrote:
> Dear staff:
> When I do the energy minimization of my system contain a protein, an ATP
> and water molecules using mdrun, it stopped at 15 steps, and return this
> messege: Steepest Descents:
>    Tolerance (Fmax)   =  1.0e+00
>    Number of steps    = 2000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -3.24259e+05 Fmax= 3.22275e+04, atom=
> 1264 Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 2.96890e +04,
> atom= 1262 Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  = -3.2425944e+05
> Maximum force =  3.2227543e+04 on atom 1264
> Norm of force =    nan
>
>
> what's wrong with it? My .mdp file is:
>
> integrator   =   steep ;minimization method
> emtol   =   1.0   ; stop minimization when max force < 1.0 KJ/mol
> nsteps   =   2000 ; max step number
> nstenergy   =   10 ;n step to write energy
> nstxtcout   =   10 ;n step to write coordinates file
>
> nstlist   =   1 ;the step to update the neighbour step list
> ns_type   =   simple; the method to determine neighbour list
> rlist   =   1.0 ;cutoff for mak e neighbour list
> coulombtype    =   cutoff ;cutoff for electrostatic force distance
> rcoulomb   =   1.0 ;long range cutoff for elect.
> rvdw   =   1.0 ; long range cutoff for vdw
> constraints   =   none ;no constraint
> pbc   =   no ; no periode boundary conditions
>
> Best wishes!

greetings,

Florian

-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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[gmx-users] a problem in the energy minimization.the

[mjduan]

Dear staff:When I do the energy minimization of my system contain a protein, an ATP and water molecules using mdrun, it stopped at 15 steps, and return this messege:Steepest Descents:   Tolerance (Fmax)   =  1.0e+00   Number of steps    = 2000Step=    0, Dmax= 1.0e-02 nm, Epot= -3.24259e+05 Fmax= 3.22275e+04, atom= 1264Step=   14, Dmax= 1.2e-06 nm, Epot=  nan Fmax= 2.96890e
 +04, atom= 1262Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1Double precision normally gives you higher accuracy.You might need to increase your constraint accuracy, or turnoff constraints alltogether (set constraints = none in mdp file)writing lowest energy coordinates.Steepest Descents converged to machine precision in 15 steps,but did not reach the requested Fmax < 1.Potential Energy  = -3.2425944e+05Maximum force =  3.2227543e+04 on atom 1264Norm of force =    nanwhat's wrong with it? My .mdp file is:integrator   =   steep ;minimization methodemtol   =   1.0   ; stop minimization when max force < 1.0 KJ/molnsteps   =   2000 ; max step numbernstenergy   =   10 ;n step to write energynstxtcout   =   10 ;n step to write coordinates filenstlist   =   1 ;the step to update the neighbour step listns_type   =   simple; the method to determine neighbour listrlist   =   1.0 ;cutoff for mak
 e neighbour listcoulombtype    =   cutoff ;cutoff for electrostatic force distancercoulomb   =   1.0 ;long range cutoff for elect.rvdw   =   1.0 ; long range cutoff for vdwconstraints   =   none ;no constraintpbc   =   no ; no periode boundary conditionsBest wishes!  

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