ithu wrote:
Hi All!
I do my md simulation but the protein moves out of the box, so it seems that
the protein is broken in .trr and .xtc file. I try to use trjconv to put the
protein back into the box and make the protein
whole. The command is like below:
trjconv -f 18pTTAD-Taz2-water.gro -s 18pTTAD-Taz2-water.tpr -pbc nojump -center
-o 18pTTAD-Taz2-water.cen.gro
However several residues still seem out of the box and the protein seem broken.
When performing g_rmsf those atoms have large rmsf (7 or 8).
If anyone could have a answer to this problem, I would be very grateful.
Quite often, several rounds of trjconv may be necessary to do various PBC,
centering, or fitting procedures. For simple proteins in water, I generally
find that
trjconv -pbc mol -ur compact -center
works fine. Note that there are numerous options for -pbc, so some
experimentation may be necessary. Also check the list archives. There are
literally thousands of posts on this very same issue, so I'm sure you'll find
something useful.
-Justin
Esteban
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El porvenir está en los huevos: bobbyybobby.blogspot.com
<http://bobbyybobby.blogspot.com>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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