On Sun, 26 Oct 2008 17:12:26 +0330
"hazizian" <[EMAIL PROTECTED]> 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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