[gmx-users] energyminimisation

[Marc Vogt]

Thank you, thank you,

I posted this question to the list a while back and got no
response.  I figured there was some possible change in the input file
but couldn't find it in the archives.  We've been worrrying about this for weeks.

Marc

> 
> 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
> >
> >
> >
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