[gmx-users] Order Parameter for HII phase

Thu Feb 23 19:25:05 CET 2017

And I agree with Piggot. The paper by Chau is about on option in g_order.

Anyway, a general question:
Can we expect to find a published article for each/some module(s) in
Gromacs?
I mean how/where can we figure out the underlying algorithm and
comprehensive description of each analysis tool?

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 ...*
>

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