[gmx-users] step size too small

[Tsjerk Wassenaar]

Minnale,

Please do read the following:

http://wiki.gromacs.org/index.php/Errors

This one's in there.

Tsjerk


On Mon, Jun 30, 2008 at 11:26 AM, minnale <minnale_gnos at rediffmail.com> wrote:
>
> Hi all,
>     1) I have embedded protein into popcbilayer
> 2) Energy minimisation
> 3) Later added ions by using genion,
> 4) When I am trying to run minimisation its showing following sentences
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 100
>
> 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 49 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -2.1825061e+05
> Maximum force    =  4.3672461e+03 on atom 7008
> Norm of force    =  5.5597691e+04
>
>
> my .mdp file is
> cpp                = /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints        =  none
> integrator          =  steep
> nsteps              =  500
> ;
> ;      Energy minimizing stuff
> ;
> emtol              =  100
> emstep              =  0.01
> nstcomm            =  1.0
> ns_type            =  grid
> rlist              =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
>
> When I run minimisation before adding ions it ran fine but later not why?
> I have searched about solve this problem in archives list and I understood
> that this not an error. Can I proceed further simulations
> Any comments will be appreciated.
>
> Thanks in advance.
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623