Thank you for your reply and help. Regards Elie
> Date: Sat, 15 Sep 2012 13:32:06 -0400 > From: jalem...@vt.edu > To: gmx-users@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 > > ======================================== > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
