[gmx-users] extracting from TRR

Matthias Ernst matthias.ernst at physik.uni-freiburg.de
Fri Sep 26 21:27:03 CEST 2014

Judging from what you wrote: Justin's answer is perfectly fine but your
understanding of RMSD obviously is not.

RMSD is not a quantity of one structure only.
Rather, it is defined as root mean square deviation (kind of a measure
of "difference") between two structures one from another. If one of
those two structures is fixed and the other a trajectory, you will get a
data set of RMSDs that monitor the difference of every snapshot in the
trajectory to the reference structure. As this seems to be what you
want, as what Justin supposed.

Regards, Matthias

On 09/26/2014 09:06 PM, niyaz.sabir wrote:
> Dear Justin,
> Thank you very much for your respond. It seems however my poor English
> put me in a spot again.
> I do not need to find the lowest RMSD frame from a trajectory, it is too
> simple even for such a dummy as I am.
> I need to find a frame that has lowest RMSD regarding to another .pdb
> file. In other words, I wish to compare the similiraty of two pdb
> structures:
> Structure A (I called it reference protein) and structure B (is to be
> extracted from md.trr). Structure B will not necessarily posses the
> lowest RMSD. The process of extracting the needed frame should be
> automatic.
> I inclined to think playing with g_confrms could help, but I do not know
> how. Help, please.
> Sincerely,
> Niyaz
> ----- Original Message ----- From: "Justin Lemkul" <jalemkul at vt.edu>
> To: <gmx-users at gromacs.org>; <niyaz.sabir at gmail.com>
> Sent: Friday, September 26, 2014 9:27 PM
> Subject: Re: [gmx-users] extracting from TRR
>> On 9/26/14 6:42 AM, N. S. wrote:
>>> Dear GMX experts,
>>> How could I extract the only state from MD-simulation .TRR (or traj.xtc)
>>> file that has the lowest RMSD from the reference protein.pdb file?
>>> Please give me a line of code in UBUNTU or the script.
>> Calculate the RMSD using g_rms, find the minimum value, then extract
>> that frame with trjconv -dump.
>> -Justin
>> -- 
>> ==================================================
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA 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
>> ================================================== 

Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611

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