[gmx-users] The sign of deuterium order parameter calculated by g_order

[Thomas Piggot]

Hi,

It outputs -Scd not |Scd|. A couple of points worth considering for your 
analysis:

Firstly, g_order/gmx order doesn't work correctly for the unsaturated 
carbons and so you will not be able to analyse the oleoly tail properly 
using the default program.

Secondly, if you are using an all-atom force field, you are better off 
using a different method. This program assumes you don't have explicit 
hydrogen atoms in your tails (as per a united-atom force field) and 
tries to predict where they will be. It does a decent job for saturated 
groups but you are better off using a method that uses the actual 
hydrogen atom positions.

For more info, you can see my recent work 
(http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00643) (apologies for 
the shamless plug!). This work also comes with a modified version of 
g_order that fixes the unsaturated carbon problems and also gives you 
the splitting of the order parameters in an CH2 group for united-atom 
force fields.

Cheers

Tom

On 22/12/17 15:15, Justin Lemkul wrote:
>
>
> On 12/22/17 10:14 AM, Jason Zhu wrote:
>> Dear All,
>>
>> I am studying the effects of cholesterols in POPC lipid bilayer. The
>> Gromacs is the version 4.6.5 in my simulations.
>>
>> By using the g_order, I could output the deuterium order parameter of 
>> POPC
>> lipids for a long-term equilibration.
>>
>> "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od 
>> deuter_sn1.xvg
>> -o order_sn1.xvg"
>>
>> The results in the file of "deuter_sn1.xvg" are given as below:
>>
>> @    title "Deuterium order parameters"
>> @    xaxis  label "Atom"
>> @    yaxis  label "Scd"
>> @TYPE xy
>>             1       0.204493
>>             2       0.223424
>>             3       0.222852
>>             4       0.228435
>>             5       0.230187
>>             6       0.229785
>>             7       0.223191
>>             8       0.217353
>>             9       0.204112
>>            10       0.193993
>>            11       0.176565
>>            12       0.162058
>>            13        0.13807
>>            14       0.112887
>>
>> As in the experimental papers about the deuterium order parameter 
>> measured
>> by NMR, the Scd is negative and round -0.2.
>>
>> I understand the sign of the deuterium order parameter is not 
>> measurable in
>> conventional NMR. I am wondering the values calculated and output by
>> g_order in Gromacs is the absolute value (|Scd|) or the opposite value
>> (-Scd) by default.
>>
>> Sorry to bother you with this simple question. But I didn't find any 
>> clear
>> answer from mail list or manual. It would be appreciated if you could 
>> give
>> your insights or comments.
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-July/114678.html 
>
>
> -Justin
>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.