[gmx-users] Order Parameter for HII phase

Justin Lemkul jalemkul at vt.edu
Thu Feb 23 19:39:17 CET 2017 


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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