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

[Sandhyaa Subramanian]

Thank you Tsjerk. Will check that out too. 
 


     On Tuesday, 24 March 2015 3:27 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
   

 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 <jalemkul at 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
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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Tsjerk A. Wassenaar, Ph.D.
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