[gmx-users] Order Parameter for HII phase

[Mohsen Ramezanpour]

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)
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. (2007)

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 ...*
>



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