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

Justin Lemkul jalemkul at vt.edu
Tue Jul 28 14:36:53 CEST 2015

On 7/28/15 1:01 AM, Carlos Navarro Retamal wrote:
> 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:
> 300K:
> Average distance:   4.090  nm
> Standard deviation: 1.451  nm
> 329K:
> Average distance:   4.134  nm
> Standard deviation: 1.515  nm

Those are pretty massive standard deviations; I wouldn't expect a membrane to 
fluctuate quite that much.  Are you averaging only the z-component of the distance?

> 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?

Your results are indistinguishable, given the huge standard deviations.


> 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.
> Best,
> Carlos
> --
> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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