[gmx-users] energy minimisation of carbon nanotubes.

[Elie M]

Thank you for your reply and help.
Regards
Elie 

> Date: Sat, 15 Sep 2012 13:32:06 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] energy minimisation of carbon nanotubes.
> 
> 
> 
> On 9/15/12 12:49 PM, Elie M wrote:
> >
> > Dear all,
> > I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ;
> >
> > ;     SWNT (10,0) on its own
> >
> > ;     Elie Moujaes, SWNT+polymers project
> >
> > ;     Energy minimization input file
> >
> > ;
> >
> > cpp                 =/usr/bin/cpp
> >
> > define              =
> > -DFLEXIBLE
> >
> > constraints         =
> > none
> >
> > integrator          =
> > cg
> >
> > nsteps              =
> > 2000
> >
> > ;
> >
> > ;     Energy minimizing stuff
> >
> > ;
> >
> > emtol               =  0.00001
> >
> > emstep              =
> > 0.03
> >
> >
> >
> > nstcomm             =
> > 1
> >
> > pbc                 =  xyz
> >
> > periodic_molecules  =  yes
> >
> > ns_type             =
> > grid
> >
> > rlist               =  1
> >
> > rcoulomb            =  1.0
> >
> > rvdw                =  1.0
> >
> > Tcoupl              =
> > no
> >
> > Pcoupl              =
> > no
> >
> > gen_vel             =
> > no
> > I have put emstep very loww toa chieve accuracy.In the output i got:
> > Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients:   Tolerance (Fmax)   =  1.00000e-05   Number of steps    =         2000   F-max             =  3.48055e+03 on atom 799   F-Norm            =  9.67779e+02
> >
> > Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1e-05
> > Double precision normally gives you higher accuracy.
> > writing lowest energy coordinates.
> > Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax < 1e-05.Potential Energy  =  8.7646348e+03Maximum force     =  1.6186214e+01 on atom 701Norm of force     =  5.4860659e+00
> > It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)?
> 
> The outcome seems reasonable.  I doubt that any algorithm, in single or double 
> precision, would ever reach Fmax < 1e-05.  Values of Fmax < 10 are generally 
> suitable for just about any purpose and Fmax < 1000 will generally result in 
> stable simulations for most systems.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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