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

Wed Jul 29 09:36:32 CEST 2015

Hi Carlos,

this *should* work. In our lab we usually look at density profiles along
the z-axis; that way you get a sense of distribution. Additionally,
depending on the size of your bilayer, you will need to correct for
undulations (non-trivial).

Peter Kroon

On 28/07/15 20:54, Carlos Navarro Retamal wrote:
> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.