[gmx-users] protein broken

[ithu]

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.

Esteban



-- 
------------------------------------------------------------
El porvenir está en los huevos: bobbyybobby.blogspot.com
------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100801/3e5f8fa6/attachment.html>