[gmx-users] Doubt in RMSD

[Justin Lemkul]

On 6/10/17 12:52 AM, Seera Suryanarayana wrote:
> Dear gromacs users,
>>
>> I have done simulations for 100ns. My peptide length is 25 residue length.
>> While calculating the RMSD by executing the gmx rms I have used 2 C-alpha
>> atoms at N-terminal and one C-alpha atom at C-terminal for least square
>> fitting and then calculated the RMSD for the rest of the C-alpha atoms.
>> Among the frames some frames got more than 2nm RMSD with respect to
>> starting structure. I have doubt here. 2nm means (20 Angstrom) is very
>> high, is it possible to get this mush deviation with respect to starting
>> structure? If it is yes, what is the reason for deviation?
>>
> 
> Have you watched the trajectory to see what happens?  Such a short peptide
> may simply unfold and the RMSD would be reasonable in that case.
> 
> -Justin
> 
> 
> Dear Justin,
> 
> The topology of the peptide is like thread, in other words the peptide is
> already unfolded (it is intrinsically disordered region). while doing
> simulations I have fixed the end residues. I have watched the trajectory in
> VMD. And there is no problem in trajectory.
> 

If it's an IDP then RMSD can be quite high as the structural has considerable 
plasticity.  RMSD is a degenerate metric; it doesn't tell you much about systems 
like these.

-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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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