[gmx-users] Measuring Bilayer thickness with gmx distance in CGMD simulations

Carlos Navarro Retamal cnavarro at utalca.cl
Tue Jul 28 07:02:12 CEST 2015

Dear gmx users,
I’m studying the implication of higher temperatures in the membrane thickness (d) of several bilayer during CGMD simulations.
In order to measure d in a pure POPC membrane i create an index group containing only PO4 beads.
Before everything, i remove PBC conditions in the simulations as following:
trjconv -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -pbc nojump -o trajout300K.xtc
trjconv -f POPC-329K-2us.xtc -s POPC-329K-2us.tpr -pbc nojump -o trajout329K.xtc

Then, I used gmx distance:
gmx distance -f trajout300K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav avg-300K
gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oav avg-329K

Finally, using g_analyse i analyse both *xvg files and i got:

Average distance:   4.090  nm
Standard deviation: 1.451  nm

Average distance:   4.134  nm
Standard deviation: 1.515  nm

Is it normal, that I’m getting a higher thickness at higher temperature? Or are my results are ‘ok', considering the values of both standard deviation?
In any case; I think this is strange, because using a different approximation/methods  (GridMAT-MD) i got at 300K, d= 3.996 and at 329K d= 3.869 ( more ‘normal’ results for this type of lipid at this temperatures).
Am i missing something with my approximation that is 'disrupting' my results?
I’ll prefer to use gmx distance to analyse d in my simulations, considering the extensive amount of time that will take me if i use GridMAT-MD to analyse my 1us of production data.
Any thoughts/suggestions are more than welcome.

Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

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