[gmx-users] Doubt in RMSD

[Seera Suryanarayana]

> 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

Dear Justin,

I have one more doubt regarding RMSD. I have executed  the following
command to calculate the RMSD.

gmx rms -s 1kr1.tpr -f 1kr1_noPBC.xtc -n index.ndx -tu ns -o rmsd.xvg

and I plotted the rmsd by xmgrace. As mentioned earlier I got more than 2nm
for some frames in the trajectory with respect to the starting structure.
When calculated the RMSD for one of the 2nm frame by using vmd or pymol I
got around 2nm of RMSD. But when I align (superimposition) one of the  2nm
RMSD frame with starting structure and If I checked RMSD, it is around 1nm.
My doubt comes here, while executing the above command whether gmx rms
consider the superimposition?

Thanks in advance
Surya
Graduate student
India.