On 4/05/2012 4:03 AM, mu xiaojia wrote:
Thanks Justin and Mark,
I compared g_rama's results for no pbc treated trajectory and pbc
treated trajectory, it seems they are the same. So gromacs' analysis
tools know how to deal with the "broken" molecules.
Caveat: some tools seem to be better than others at dealing with PBC.
There are known question marks hovering over g_dist, g_bond and
g_mindist. This situation is probably a consequence of different tools
being developed at different times during the evolution of the software
suite.
Mark
But if one want to extract such coordinates out for computing it
myself, it is necessary to -pbc mol first, otherwise the molecules
might be "broken" for calculating scripts like matlab.
good to know this, thanks!
On Wed, May 2, 2012 at 8:03 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 03/05/12, *mu xiaojia *<muxiaojia2...@gmail.com
<mailto:muxiaojia2...@gmail.com>> 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)?
That entirely depends on what you are trying to observe. You may
find you need multiple representations of the trajectory for
different purposes.
(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.
If molecules diffuse across the periodic boundaries, you cannot
have a single representation that is both compact and lacks jumps.
Mark
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