[gmx-users] Order Parameter for HII phase
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Fri Feb 24 00:55:15 CET 2017
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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>>>>>
>>>>
>>>>
>>>> --
>>>> *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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