[gmx-users] trjorder

[Justin Lemkul]

On 1/30/14, 1:57 AM, shahab shariati wrote:
> Dear Justin
>
> Thanks for your reply.
>
> My system contains dopc lipid. ns.xtc and ns.tpr files contain all atoms
> related to dopc molecule.
>
> I want to obtain number of atoms in a first group (C38 atom in dopc) which
> are located in special distance (0.74 nm) of the second group (rest of
> atoms in dopc).
>
> I put 2 groups in the ns.ndx file: 1) C38 atoms and 2) rest of atoms.
>

What does "rest of atoms" mean?  Is the the whole system?  Just the atoms of 
DOPC?  Is the content of ns.xtc just a subset of what is found in the .tpr file, 
i.e. through the use of xtc-grps in the .mdp file?  In order for trjorder to 
work, you likely need matching information between .xtc and .tpr, at minimum.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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