[gmx-users] lipid membrane slicing

[Justin A. Lemkul]

Poojari, Chetan wrote:
> Hi Justin,
> 
> I used the below g_select command to get the list of phosphorus atoms (from DPPC lipid) within 0.5 nm of protein. 
> 
> g_select -f ordered.xtc -n initial.ndx -on select.ndx -select "name P and within 0.5 of group Protein" -s md_500ns.tpr -b 100000 -dt 1000
> 
> My output is an index file which contains different phosphorus atom number at each frame within 0.5nm of protein and this number changes for every frame.
> 
> Please can I know if its possible to use this index file to convert each frame into trajectory file and do analysis for lipids within 0.5 of protein.
> 

Yes, but not in an automatic way.  Each index group corresponds to the atoms 
that satisfy the given criterion in a given frame.  You can parse these atoms 
from the trajectory by writing individual snapshots by selecting each of the 
indices for each of the frames.  Then you might be able to use trjcat to stitch 
a trajectory back together, but if there are different numbers of atoms in 
different frames, the trajectory will be invalid.

-Justin

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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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