On 25/10/2011 5:29 PM, James Starlight wrote:
This was due to that in .gro file corresponded to the end of
productive MD I've found this
http://i1209.photobucket.com/albums/cc394/own11/mdL.png
It's looks like the protein moved out from box so I've thought that
some error occured during stimulation
There's no outside to a periodic cell - you will find a matching cavity
on the other side of the triclinic periodic cell, where some of the
solute atoms actually are also....
GROMACS uses the triclinic representation internally for efficiency - a
2D analogy is that a hexagon tiling a plane can be converted to a
rhombus tiling the plane. It doesn't bother wasting your valuable
computing cluster time converting back to the initial representation,
which probably wasn't wanted. That is, mdrun makes no attempt to guess
how you would like your output to appear. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for ideas about how to make your output look as you would like.
Mark
I don't understand this statement. You should also note that a
periodic box has no "outside." Perhaps it would be useful to post
images online. If you choose to do so, please follow bullet point
#4 here:
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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