[gmx-users] energyminimisation

[cpchng at bii-sg.org]

Hi Smith,

   It's such a coincidence!
I'm facing the exact same problem right now!

I did a search of the mailing list archive and found David's Feb 11th
posting:
http://www.gromacs.org/pipermail/gmx-users/2004-February/035880.html

For 3.2.1, you have to use:
define = -DFLEXIBLE
instead of
define = -DFLEX_SPC

I just tried these 2 variants with Gromacs 3.2.1 on my system and indeed with
FLEXIBLE, EM now works as per version 3.1.5_pre1 while FLEX_SPC gave
the same error as below.


cheers,
choon-peng
-------
Singapore

> dea all,
> I am using gromacs-3.2.1 for simulating a protein.I used the em.mdp file
> given there.when i tried to energy minimize the protien it gives the
> following error
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
>
> 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 53 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  = -3.1566375e+05
> Maximum force     =  2.8458027e+03 on atom 1650
> Norm of force     =  1.7127547e+05
>
>
> This is the input file i gave,
> **********************************************************************************
>
>         User spoel (236)
> ;       Wed Nov  3 17:12:44 1993
> ;       Input file
> ;
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  1000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
>
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> *********************************************
> Is this wrong,has the protein not energy minimized sufficiently.please
> tell what should be done?
> cheers
> smith
>
>
>