[gmx-users] Order Parameter for HII phase

Tue Oct 24 19:32:28 CEST 2017

Hi Everyone,

Like to know your thoughts on this.
I appreciate any comment on this in advance.

Cheers,
Mohsen

On Wed, Oct 18, 2017 at 7:26 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Justin, Tom, Antonio,
>
> I read the articles recommended in the previous emails.
> To get the order parameter, for any system and by any technique (e.g.
> g_angle), we need to calculate the C-D vector angle with respect to the
> "local normal vector" at the place of that lipid.
>
> For the bilayer, it is the Z direction which is the normal vector to the
> bilayer surface. Easy.
>
> For the HII, however, this "local normal vector" is challenging.
> The cylinders in HII (which is long enough) are not perfect cylinders and
> are bent (in a shape like a Tilda "~" ). Even when the cylinders are not
> bent (i.e.they are like "__", still a "local normal vector" need to be
> calculated in this calculation.
>
>
> Here are four solutions I am thinking about:
>
> 1) Using the "radial" option in g_order, but I am not sure if this will
> give what I want.
>
> 2) Slicing the HII cylinders in Z direction (i.e. the cylinder axis),
> calculating a center of mass for those lipids in each slice, and then using
> the g_angle and its "-g2 sphnorm". In this way, the COM of that slice will
> be taken as the center of the sphere (an approximation).
>
> 3) Using g_angle but using "-g1 plane": in this case, the coordinates of
> three atoms in that lipid at each frame will be used to make the local
> normal vector.
>
> 4) Maybe a combination of g_sgangle and g_angle/g_order. The
> g_sgangle seems to give the local normal vector for each time frame. This
> can be subsequently used in g_order or g_angle for angle calculation.
>
> One of the main problems in methods 3 and 4 is that: the way the three
> atoms on the lipid are selected, the normal vector will be different,
> especially if the lipid is tilted.
>
> Is there any other way which I could calculate the C-D angle and order
> parameter in HII phase?
>
> Please let me know your opinion. Any help is appreciated in advance.
>
> Cheers,
> Mohsen
>
> On Thu, Feb 23, 2017 at 4:55 PM, Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com> wrote:
>
>> Thanks Antonio.
>> I will give them a try :-)
>>
>> Cheers
>> Mohsen
>>
>> On Thu, Feb 23, 2017 at 4:15 PM, Antonio Baptista <baptista at itqb.unl.pt>
>> wrote:
>>
>>> Hi Mohsen,
>>>
>>> I suggest you have a look at the QRB 1977 review by Seelig, that Tom
>>> already mentioned. Like for the planar case, they discuss how spectra of
>>> cylindrical lipid phases are related to the order parameter tensor (but I
>>> never looked into the details for that case). Anyway, I don't know if you
>>> want to compare your simulations with experimental data or are just looking
>>> for a convenient structural parameter. But, whatever the case is, reading
>>> the literature and thinking about the geometry of your system (Duliez's
>>> papers are a good train for that) should give you some hints for a relevant
>>> parameter for your system.
>>>
>>> Once you have selected a parameter, you can compute it from stratch
>>> using other GROMACS tools besides g_order. In particular, you can use
>>> g_gangle to get several sorts of angles and then process them yourself. As
>>> an example, you can use this approach to compute SCD using the equation
>>> already mentioned by Tom, and then check if it agrees with the SCD given by
>>> g_order (I once did that, just to be sure).
>>>
>>> Good luck! :)
>>>
>>> Best,
>>> Antonio
>>>
>>>
>>>
>>> On Thu, 23 Feb 2017, Justin Lemkul wrote:
>>>
>>>
>>>>
>>>> On 2/23/17 1:25 PM, Mohsen Ramezanpour wrote:
>>>>
>>>>> And I agree with Piggot. The paper by Chau is about on option in
>>>>> g_order.
>>>>>
>>>>>
>>>> Yes, and if memory serves (been a while since I used the program, so
>>>> perhaps I am confusing something), this is what -o provides you so I
>>>> thought it was relevant.  -od gives you the deuterium order parameters.
>>>> The documentation for gmx order is indeed very sparse.
>>>>
>>>> Anyway, a general question:
>>>>> Can we expect to find a published article for each/some module(s) in
>>>>> Gromacs?
>>>>>
>>>>
>>>> No.  Many of the tools are just implementations of simple algorithms
>>>> used widely in simulations.  Some do have specific references and those are
>>>> generally printed to the screen output in bold blocks of text.
>>>>
>>>> With regards to deuterium order parameters, there is a well accepted
>>>> and ubiquitously used equation, which Tom posted.
>>>>
>>>> I mean how/where can we figure out the underlying algorithm and
>>>>> comprehensive description of each analysis tool?
>>>>>
>>>>>
>>>> That's why GROMACS is open source :)  Efforts are certainly always made
>>>> to provide references when possible.
>>>>
>>>> -Justin
>>>>
>>>> Cheers
>>>>> Mohsen
>>>>>
>>>>>
>>>>> On Thu, Feb 23, 2017 at 10:06 AM, Mohsen Ramezanpour <
>>>>> ramezanpour.mohsen at gmail.com> wrote:
>>>>>
>>>>> Hi Justin, Piggot,
>>>>>>
>>>>>> Thanks for your replies.
>>>>>> I agree with that. The problem is that the situation is
>>>>>> straightforward
>>>>>> for bilayers as bilayers are usually in specific angles regarding the
>>>>>> magnetic field (e.g. they are perpendicular, as it is the case in
>>>>>> Vermeer study.)
>>>>>> For example the normal to the bilayer is z and we do not need be worry
>>>>>> about anything else.
>>>>>> However, in the case of HII phase, there are cylinders which are not
>>>>>> perfectly cylinder.
>>>>>> Even if they are perfect cylinders, I think I should use "membrane
>>>>>> radial
>>>>>> axis" to mimic the local normal vector to the lipid surface.
>>>>>>
>>>>>> Cheers
>>>>>> Mohsen
>>>>>>
>>>>>>
>>>>>> On Thu, Feb 23, 2017 at 8:08 AM, Piggot T. <T.Piggot at soton.ac.uk>
>>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>>
>>>>>>> I don't believe this Chau paper is for deuterium order parameters
>>>>>>> (as I
>>>>>>> think you are most likely referring to) but is related to some of
>>>>>>> the other
>>>>>>> order parameter options in gmx order. The Vermeer paper you mention
>>>>>>> gives a
>>>>>>> good overview of deuterium order parameters and you can find more
>>>>>>> details
>>>>>>> in the papers referenced therein (e.g. the Douliez et al. and the
>>>>>>> Seelig et
>>>>>>> al. papers in particular).
>>>>>>>
>>>>>>> For united-atom systems (as gmx order assumes), I believe the
>>>>>>> calculation
>>>>>>> is performed in gmx order using the "SCD = (2/3) Sxx + (1/3) Syy"
>>>>>>> equation
>>>>>>> (which is nicely derived in the 1998 Douliez paper:
>>>>>>> http://aip.scitation.org/doi/pdf/10.1063/1.476823) . The calculation
>>>>>>> requires an appropriate definition of the molecular frame of the
>>>>>>> system,
>>>>>>> where the z-axis is the bilayer normal.
>>>>>>>
>>>>>>> Note that if you are calculating order parameters for unsaturated
>>>>>>> carbons
>>>>>>> (e.g. as in carbon-carbon double bonds), gmx order doesn't currently
>>>>>>> do
>>>>>>> this correctly as it requires a different calculation with a
>>>>>>> different
>>>>>>> molecular frame.
>>>>>>>
>>>>>>> Cheers
>>>>>>>
>>>>>>> Tom
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
>>>>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of
>>>>>>> Justin
>>>>>>> Lemkul [jalemkul at vt.edu]
>>>>>>> Sent: 23 February 2017 12:16
>>>>>>> To: gmx-users at gromacs.org
>>>>>>> Subject: Re: [gmx-users] Order Parameter for HII phase
>>>>>>>
>>>>>>> On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote:
>>>>>>>
>>>>>>>> Dear Gromacs users,
>>>>>>>>
>>>>>>>> Unfortunately, I did not get any reply on this post.
>>>>>>>>
>>>>>>>> I was wondering if anyone is aware of the original paper on g_order
>>>>>>>> so
>>>>>>>>
>>>>>>> that
>>>>>>>
>>>>>>>> I can understand the underlying algorithm of the options?
>>>>>>>> I am not sure how to use it for HII phase order parameters.
>>>>>>>>
>>>>>>>> I found this article but I am not sure if these are the ones, as
>>>>>>>> they do
>>>>>>>> not describe g_order.
>>>>>>>>
>>>>>>>> "A new order parameter for tetrahedral configurations" by Chau and
>>>>>>>>
>>>>>>> Hardwick
>>>>>>>
>>>>>>>> (1998)
>>>>>>>>
>>>>>>>
>>>>>>> This is the reference given at the end of the gmx order help
>>>>>>> description.
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> and
>>>>>>>> "Acyl chain order parameter profiles in phospholipid bilayers:
>>>>>>>>
>>>>>>> computation
>>>>>>>
>>>>>>>> from molecular dynamics simulations and comparison with 2 H NMR
>>>>>>>>
>>>>>>> experiments"
>>>>>>>
>>>>>>>> by Vermeer et al.
>>>>>>>>
>>>>>>>> Thanks in advance for your comments
>>>>>>>> Mohsen
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sun, Feb 19, 2017 at 10:18 AM, Mohsen Ramezanpour <
>>>>>>>> ramezanpour.mohsen at gmail.com> wrote:
>>>>>>>>
>>>>>>>> Hi Everyone,
>>>>>>>>>
>>>>>>>>> I was wondering if someone has any suggestion on the following
>>>>>>>>> post,
>>>>>>>>> please?
>>>>>>>>>
>>>>>>>>> Cheers
>>>>>>>>> Mohsen
>>>>>>>>>
>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>>>>>>>>> Date: Thu, Feb 16, 2017 at 3:13 PM
>>>>>>>>> Subject: Order Parameter for HII phase
>>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Dear Gromacs users,
>>>>>>>>>
>>>>>>>>> I am interested in calculation of order parameter of lipids in a
>>>>>>>>> HII
>>>>>>>>>
>>>>>>>> phase.
>>>>>>>
>>>>>>>>
>>>>>>>>> I am not sure about the correct command to use. Which one of the
>>>>>>>>>
>>>>>>>> following
>>>>>>>
>>>>>>>> should I use to be able to compare my data with deutirated NMR
>>>>>>>>>
>>>>>>>> experiments?
>>>>>>>
>>>>>>>>
>>>>>>>>> 1) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o
>>>>>>>>> order.xvg  -od
>>>>>>>>> deuter.xvg  -d z  -szonly
>>>>>>>>>
>>>>>>>>> or
>>>>>>>>>
>>>>>>>>> 2) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o
>>>>>>>>> order.xvg  -od
>>>>>>>>> deuter.xvg  -d z
>>>>>>>>> (In this case, there are four columns of data (x, y, z for each
>>>>>>>>> carbon
>>>>>>>>> atom).
>>>>>>>>> The column 3 seems to be the same with when we include -szonly)
>>>>>>>>>
>>>>>>>>> or anything else?
>>>>>>>>>
>>>>>>>>> Corresponding available experimental data, I assume the second
>>>>>>>>> command
>>>>>>>>> should be correct in my case . However, I am not sure x or y or
>>>>>>>>> what
>>>>>>>>>
>>>>>>>> to use
>>>>>>>
>>>>>>>> for judging.
>>>>>>>>>
>>>>>>>>> Cylinders in HII phase are parallel to the Z axis in my system.
>>>>>>>>>
>>>>>>>>> Many thanks in advance for your comments
>>>>>>>>> Mohsen
>>>>>>>>> --
>>>>>>>>> *Rewards work better than punishment ...*
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> *Rewards work better than punishment ...*
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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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>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *Rewards work better than punishment ...*
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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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>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>

-- 
*Rewards work better than punishment ...*