Hey :) trjconv also has an option -drop file.xvg with -dropover/-dropunder, which allows writing out frames based on, e.g., RMSD.
Cheers, Tsjerk On Tue, Mar 24, 2015 at 1:59 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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 > > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.