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

Tue Jul 28 20:54:32 CEST 2015

Hi Teemu,
Thanks for the reply.
Unfortunately, i cannot upgrade to 5.0.6 right now ( i have to ask to the admin of the cluster first, and so on and so far).
I do can downgrade to 4.6.3 and use g_dist instead.
I have read some papers where people claimed to have been used g_dist to measure the thickness of a bilayer, but I wasn’t capable to do that.
I created 3 different groups:
All PO4 beads of the bilayer: G1
PO4 beads of the top leaflet of the bilayer: G2
PO4 beads of the bottom leaflet of the bilayer: G3
but considering that g_dist used the COM of the groups when i used g_dist as following:
g_dist -f POPC-300K-2us.xtc -s POPC-300K-2us.tpr -n index.ndx -o PO4-distance

If i select group 1 and 2 as group G1 i got a distance of 0 (which i think it make sense, considering that g_dist use the COM of a group)
but when i select group 1: G2 and group 2: G3 (PO4 beads of the top  and bottom leaflet respectively) i got really nice values:
~3.9 at 300K
~3.8 at 328K
with an standard deviation of ~0.002 each (considering the Z component, of course)
Are this results ok? Can i use this approximation  (measuring the distance between the top and bottom PO4 beads of a bilayer) to get the membrane thickness of a bilayer?
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 3:17:47 PM, Teemu Murtola (teemu.murtola at gmail.com<mailto:teemu.murtola at gmail.com>) wrote:

Please upgrade to 5.0.6. There was a bug with gmx distance -oxyz that
caused the output file to not appear (or to overwrite some unintended
files), which was fixed for the latest version.

On Tue, Jul 28, 2015, 17:34 Carlos Navarro Retamal <cnavarro at utalca.cl>
wrote:

> 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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