[gmx-users] energy minimization output

[Archana Sonawani]

Dear Erik,

I also encountered similar problem. So you mean it cannot be further energy
minimized? How can we proceed with NPT if the system is not in equilibrium?

On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

>
> 26 sep 2012 kl. 08.16 skrev Shima Arasteh:
>
> > Dear all,
> >
> > My system contains lipids, protein and water.
> > I want to energy minimize it, so ran grompp:
> >
> >
> > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
> >
> > and then:
> > # mdrun -v -deffnm em
> >
> >
> > The output is:
> > Steepest Descents:
> >    Tolerance (Fmax)   =  1.00000e+03
> >    Number of steps    =        50000
> > Step=   14, Dmax= 1.2e-06 nm, Epot=  2.30004e+17 Fmax=         inf,
> atom= 518
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 1000
> >
> > 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.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.3#
> >
> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  =  2.3000388e+17
> > Maximum force     =            inf on atom 518
> > Norm of force     =            inf
> >
> >
> > Why the maximum force and norm of it is not written? I repeated it for a
> few times, but no difference.
> >
> >
>
> It's written. Unfortunately it's infinite.
>
> >
> > Thanks for your suggestions in advance.
> > Sincerely,
> > Shima
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> -----------------------------------------------
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 6688        fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339