[gmx-users] RMSD plot

[Mark Abraham]

On 30/07/2012 3:39 AM, tarak karmakar wrote:
> Dear All,
>
> In my initial protein pdb structure I have added some external ligand
> molecules and as a result of that there are several short contacts.
> So, well, I minimized the system and then got the 'prot_min.gro' file.
> Now after the equilibration run, I plotted the RMSD of the resulting
> trajectory with respect to the initial pdb structure. So as the pdb
> had some short contacts, the resulting RMSD is showing large
> increasing value around 0.4-0.5 nm.
>
> 1) Then, is it better to plot [ for reporting purpose ] the RMSD of
> the trajectory with respect to the minimized coordinate file rather
> than w. r. t. the initial PDB file?

Since neither of those configurations were sampled from the target 
ensemble, it's a bit hard to say they make good reference states. Doing 
initial MD with position restraints on the protein stops it moving much 
while the ligand gets sorted out. Use that as the reference state from 
which you begin production MD.

Better still, stop and consider how you will analyse your results before 
you begin your simulation. Then you're better placed to do a simulation 
that will lead to a meaningful result.

> 2) What is the acceptable range of RMSD for a protein simulation ? (
> below 0.2 nm !! )

It depends on a whole host of things. There's no magic number.

Mark