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

[Carlos Navarro Retamal]

Hi Justin,
thanks for your reply.
Is there a way, to analyse each component (x,y,z) of the distance without the flag -oxyz?
For some reason, I’m unable to get this data with gmx distance.
In fact, when i ran
gmx distance -f trajout329K.xtc -s POPC-329K-2us.tpr -n index.ndx -oxyz
the command line doesn’t generate anything (any *xvg file).
I don’t know what I’m doing wrong
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



On July 28, 2015 at 9:34:32 AM, Justin Lemkul (jalemkul at vt.edu<mailto:jalemkul at vt.edu>) wrote:

July 28, 2015 at 6:09:51 AM GMT-3 ro 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.

-Justin

> 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
http://mackerell.umaryland.edu/~jalemkul

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