[gmx-users] Deuterium order parameter for DPPC

[Justin Lemkul]

On 1/27/16 1:01 AM, Him Shweta wrote:
> Thank you so much Justin for your reply, I am so sorry it is DOPC not DPPC
> , i did a mistake while posting the querry.
> When i am calculating order parameter for DOPC i am getting order parameter
> values only for 16 atoms. But in several papers (J. Chem. Theory. Comput.
> 2012, 8, 2938-2948) order parameter for 17 atoms is reported for DOPC
> instead of 16 atoms (as what i am getting in my calculation). As you said,
> since the ester C won't have one and the terminal methyl is not calculated
> so the total no. of carbon for which the order parameter is printed is 16.
> This is what i am getting in my calculation. But people have reported order
> parameter for 17 atoms. Please help.
>

They must be using other software, and I'm not sure how the terminal methyl is 
calculated.  With gmx order the axis is defined as the previous (n-1) and next 
(n+1) carbon atom.  For a terminal methyl, no such axis can be defined.  I doubt 
it has any implications on your findings; though I'm not sure if the gmx order 
bug related to unsaturated chains was ever fixed.  Note the use of -unsat and 
several mailing list postings related to it.  DPPC is very different from DOPC 
in this regard.

-Justin

>>
>>
>>> Groupname: C31 First atomname: C31 First atomnr 93
>>> Groupname: C32 First atomname: C32 First atomnr 95
>>> Groupname: C33 First atomname: C33 First atomnr 145
>>> Groupname: C34 First atomname: C34 First atomnr 148
>>> Groupname: C35 First atomname: C35 First atomnr 151
>>> Groupname: C36 First atomname: C36 First atomnr 154
>>> Groupname: C37 First atomname: C37 First atomnr 157
>>> Groupname: C38 First atomname: C38 First atomnr 160
>>> Groupname: C39 First atomname: C39 First atomnr 163
>>> Groupname: C310 First atomname: C310 First atomnr 165
>>> Groupname: C311 First atomname: C311 First atomnr 167
>>> Groupname: C312 First atomname: C312 First atomnr 170
>>> Groupname: C313 First atomname: C313 First atomnr 173
>>> Groupname: C314 First atomname: C314 First atomnr 176
>>> Groupname: C315 First atomname: C315 First atomnr 179
>>> Groupname: C316 First atomname: C316 First atomnr 182
>>> Groupname: C317 First atomname: C317 First atomnr 185
>>> Groupname: C318 First atomname: C318 First atomnr 188
>>>
>>> Read trajectory. Printing parameters to file
>>> Atom 1 Tensor: x=-0.265441 , y=0.280524, z=-0.0150827
>>> Atom 2 Tensor: x=-0.216881 , y=-0.206841, z=0.42372
>>> Atom 3 Tensor: x=-0.24463 , y=0.182178, z=0.0624524
>>> Atom 4 Tensor: x=-0.199236 , y=-0.146768, z=0.346004
>>> Atom 5 Tensor: x=-0.203594 , y=0.13677, z=0.0668253
>>> Atom 6 Tensor: x=-0.163806 , y=-0.124917, z=0.288722
>>> Atom 7 Tensor: x=-0.128688 , y=0.147232, z=-0.0185443
>>> Atom 8 Tensor: x=-0.101921 , y=-0.190463, z=0.292384
>>> Atom 9 Tensor: x=-0.103099 , y=0.120349, z=-0.01725
>>> Atom 10 Tensor: x=-0.0401138 , y=-0.128687, z=0.168802
>>> Atom 11 Tensor: x=-0.0962026 , y=0.0380915, z=0.0581114
>>> Atom 12 Tensor: x=-0.0915375 , y=-0.0573191, z=0.148856
>>> Atom 13 Tensor: x=-0.103044 , y=0.0322047, z=0.0708399
>>> Atom 14 Tensor: x=-0.0852172 , y=-0.0285316, z=0.113749
>>> Atom 15 Tensor: x=-0.0829265 , y=0.0244509, z=0.0584748
>>> Atom 16 Tensor: x=-0.0590676 , y=-0.00856891, z=0.067636
>>
>>
>>

-- 
==================================================

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

==================================================