[gmx-users] protein broken

[Justin A. Lemkul]

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

-- 
========================================

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

========================================