[gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value

[Justin Lemkul]

On 3/23/15 8:32 AM, Sandhyaa Subramanian wrote:
> Dear all,
> I have a trajectory of 10,000 frames (traj.xtc) and would like to create a new sub-trajectory (sub_traj.xtc) by extracting specific frames from traj.xtc based on certain RMSD cut-off value to the reference PDB file. For example, if my RMSD cut-off is 0.3 nm, then I would like to extract all frames from traj.xtc that have RMSD less than or equal to 0.3nm with the reference PDB file.
> Will g_cluster -f traj.xtc -s reference.pdb -n index.ndx -cutoff 0.3 -fit -o newtraj help me? I mean can I use newtraj.xpm file in the trjconv (under -sub) command to get my desired result?

An .xpm file is a matrix file; it's not a viable input for trjconv.

Write out the RMSD time series (g_rms), use grep/awk to find which frames 
correspond to values under your cutoff, and pass those to trjconv -dump to write 
out individual frames of interest.  Concatenate with trjcat.

-Justin

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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

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