[gmx-users] Selecting certain types of atoms from trajectory file with C++ code

Justin Lemkul jalemkul at vt.edu
Thu Sep 19 13:52:06 CEST 2013

On 9/19/13 12:33 AM, Zhikun wrote:
> Dear users,
> Recently I have been trying to use "xdrfile" libray to read trajectory
> ".trr" file in my own C++ code. Now I can just read the coordinates of  all
> atoms at each time frame. But I don't know how to select certain types of
> atoms from the trajectory file. Although the graomcs tool "make_ndx" can do
> this, but i need to do it with C++ codes for the purpose of further
> analysis. Does someone have any experience about this? Your reply would be
> greatly appreciated.

Atom names, types, etc are not stored in trajectories at all.  They are in 
topologies (.top/.tpr) so you need to get the information from those file types.



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


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