On 5/2/12 8:55 PM, mu xiaojia wrote:
Dear gmx users,
I have a question about using the trjconv -pbc options before analyzing my
trajectory. It's stated by Justin's tutorial that:
"use trjconv to account for any periodicity in the system. The protein will
diffuse through the unit cell, and may appear to "jump" across to the other
side of the box. To account for such actions, issue the following:
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact"
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html
)
But for my system, I study the short peptides' aggregation, I have many
short peptides(not one or two single proteins) and waters, when I use -pbc
nojump to treat my trajectory, it only gives me correct short peptides(no
across out of the box), but the water is quite diffused. (I guess it is
different with the tutorial since on it the protein is 1 or 2 polymers)
So (1)how should I analyze such results if I want to study both short
peptides(correct coordinates, no crossings) and waters(diffused and crossed
box)?
(2) I tried all the pbc options(even try them one after another, like mol
first, nojump second), currently no clues of how to get both peptides and
waters correct at the same time.　Command for correct protein but incorrect
waters' coordinates is:
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump
Thanks very much, I appreciate any suggestions.
In general:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
For your system, I'd create an index group specifying a single peptide that will
be convenient to locate in the center of the box. Center on it using the
-center option of trjconv. You can do it all in one shot for simple systems of
a couple peptides with trjconv -center -pbc mol -ur compact.
Note that these "corrections" for PBC are only necessary for visualization, not
the analysis itself.
-Justin
--
========================================
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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