[gmx-users] Order Parameter for HII phase
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Thu Oct 19 03:26:24 CEST 2017
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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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>>>>>> * Please search the archive at http://www.gromacs.org/Support
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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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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>
>
>
> --
> *Rewards work better than punishment ...*
>
--
*Rewards work better than punishment ...*
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