[gmx-users] (no subject)
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Fri Feb 14 11:05:26 CET 2003
> 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
> 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
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