[gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 120

[Him Shweta]

Thank you so much Justin for your help.


>    3. Re: Deuterium order parameter for DPPC (Justin Lemkul)
>
> Message: 3
> Date: Wed, 27 Jan 2016 07:41:11 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Deuterium order parameter for DPPC
> Message-ID: <56A8BAE7.8090603 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>
> ==================================================
>
>