[gmx-users] (no subject)

[Nguyen Hoang Phuong]

> Nguyen Hoang Phuong wrote:
>
>
> > first, you have to use double precision.
> > Here is an example of mdp file.
> > title                    = protein in water
> > cpp                      = /lib/cpp
> > include                  = -I../top
> > define                   = -DFLEX_SPC
> > integrator               = cg
> > emtol                    = 0.000001
> > emstep                   = 0.000001
> > nstcgsteep               = 100
> > nsteps                   = 500000
> > nstxout                  = 50
> > xtc_grps                 = Protein
> > energygrps               = Protein
> > nstlist                  = 10
> > ns_type                  = grid
> > rlist                    = 1.4
> > vdwtype                  = Shift
> > coulombtype              = PME
> > rcoulomb                 = 1.4
> > rvdw                     = 1.4
>
>
> hmm, I don't think PME should be used in NM, either in vacuum or a water shell.
> The interactions with the (infinite number of) periodic images would
> be artificial (and more harmful than in a solvent MD simulation, with the
> screening effect of the water instead of the vacuum here). Moreover, the
> interactions with the periodic images might make the minimization less stable.
>
> Better use a large enough cutoff, to include the whole system
> (AND a large enough box to prevent interactions with periodic images, or
> switch off PBC alltogether).
>
>
> >
> > in vacuum, you can easily get the mimimum energy structure but in
> > water it will take a lot of time. You can look at the value of Fmax which
> > is printed out for every step. If Fmax<10^5 then you may have the optimal
> > structure.
>
> that should be a 10^-5 I guess?
>

In vacuum I alway used cut-off and in water, PME or cut-off yields almost
the same results of eigenvectors and eigenvalues( at least for my small
peptide).

yes, Fmax<10^-5

> --
>
> Bert
>
> ____________________________________________________________________________
> Dr. Bert de Groot
>
> Max Planck Institute for Biophysical Chemistry
> Theoretical molecular biophysics group
> Am Fassberg 11
> 37077 Goettingen, Germany
>
> tel: +49-551-2011306, fax: +49-551-2011089
>
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
> ____________________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>