[gmx-users] extracting from TRR

niyaz.sabir niyaz.sabir at gmail.com
Fri Sep 26 23:30:33 CEST 2014

Dear Matthias,

I am very new ( about 1 month only) to MD and Dr. Justin A. Lemkul is 
well-known expert in MD, the author of excellent Gromacs tutorials.
Certainly, I do not understand  well even basics of Gromacs. And namely this 
is the reason why I have subscribed to gromacs.org_gmx-users mailing list, 
to learn from much more experienced colleagues. And I think this is quite 
normal (asking questons),

----- Original Message ----- 
From: "Matthias Ernst" <matthias.ernst at physik.uni-freiburg.de>
To: <gmx-users at gromacs.org>; "niyaz.sabir" <niyaz.sabir at gmail.com>
Sent: Saturday, September 27, 2014 12:26 AM
Subject: Re: [gmx-users] extracting from TRR

> 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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