Open ErikPoppleton opened 3 days ago
Hey Erik, so far I was not able to reproduce this. I added a folder "examples/thickness" with a small example: there I seem to get consistently all lipids as expected. Could you share a small snippet of trj where the issue occurs?
For -nonflat
only one atom per lipid should be selected
It appears to happen when you have a raw trajectory and pick whole lipid tails instead of just terminal carbons. I have attached an example with a 5-frame trajectory where it happens on the 3rd frame.
For "one atom per lipid", does that means one atom per tail, or only one atom total? I switched doing one atom per tail because that's much easier to select (and seems to work?), but I can figure out how to do just one between the two tails as well.
Thanks for the very useful tool!
I am trying to get the thickness of a simulation of a DOPC membrane over time. I first made an index file with all the phosphates and lipid tails selected (groups 'PA' and 'OL') and then used that as input for
g_lomepro
:{ echo -e "PA"; echo -e "OL"; } | ~/software/g_lomepro/g_lomepro_static -b 0 -e 500000 -f md.xtc -n lomepro.ndx -s md.gro -apl apl1 -thick thick1 -curve curve1 -lip_num 898 -nonflat -binx 100 -biny 100
However in the
thick1.out_over_time.dat
file, there are not always 898 entries per time step. Can you explain why in some time steps some of the phosphate IDs are missing from the thickness?Also am I correct that when I choose the
-nonflat
option, I'm supposed to have a group containing the whole lipid tails, or is it supposed to be just the last atom in each tail? The paper and the help say different things.