[gmx-users] The sign of deuterium order parameter calculated by g_order
t.piggot at soton.ac.uk
Fri Dec 22 17:42:47 CET 2017
It outputs -Scd not |Scd|. A couple of points worth considering for your
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
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
>> lipids for a long-term equilibration.
>> "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od
>> -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
>> 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
>> answer from mail list or manual. It would be appreciated if you could
>> your insights or comments.
Dr Thomas Piggot
University of Southampton, UK.
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