[gmx-users] Pr reach and not reach to equilibria

Xavier Periole X.Periole at rug.nl
Sun Oct 26 14:30:05 CET 2008

On Sun, 26 Oct 2008 17:12:26 +0330
  "hazizian" <hazizian at razi.tums.ac.ir> wrote:
> Hi gromacs users 
> I have done Position restrain for 50 ps. 
> after it had finished, I checked the rmsd for confident that rms reached to 
> it's equilibrate mode. When I check it by g_rms command and select system 
> subgroup, I find that it had not reached to equilibria, but after I check  
> It by protein or protein-H or any subgroup, I saw that rmsd reached to Plato 
> after 5 ps, and when I checked it by Sol subgroup it had not reached,my 
> question is, can I use the result of this pr for md or I must continue it 
> until the whole system (protein  sol) reaches to equilibria 
> thank's 
You do not say to which group you are applying the position restrains!
If it is on a set of atoms of the protein then what you observe is ok.
It is unlikely that you have any interest in applying PR to the solvent.
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
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XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

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