[gmx-users] trjconv correct the pbc before analysis

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 4 03:25:36 CEST 2012

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 


> 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.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>> wrote:
>     On 03/05/12, *mu xiaojia *<muxiaojia2010 at gmail.com
>     <mailto:muxiaojia2010 at 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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