[gmx-users] protein broken

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 1 20:11:46 CEST 2010

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.


> Esteban
> -- 
> ------------------------------------------------------------
> El porvenir está en los huevos: bobbyybobby.blogspot.com 
> <http://bobbyybobby.blogspot.com>
> ------------------------------------------------------------


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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