[gmx-users] Deuterium order parameter for DPPC

[Justin Lemkul]

On 1/26/16 6:26 AM, Him Shweta wrote:
> Hello Everyone,
>
> I am facing a problem while calculating the order parameter in case of
> DPPC.
> I have defined the atom in the index file properly. But the problem is that
> i have defined atom index for 18 atoms and m getting order parameter for
> only 16 atoms. I am not getting what mistake i have done. Please suggest..
> I have attached the index file .
>

The acyl chain (palmitoyl) in DPPC has only 16 carbons, so I don't know how/why 
you've set up 18.  From those, you can only get 14 order parameters, since the 
ester C won't have one and the terminal methyl is not calculated.

Check your index groups; you're doing something wrong in setting those up.  Note 
the list does not accept attachments, so we can't check your groups.

-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=0.0676363
>
>
>

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

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

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