On 30/07/2012 4:49 PM, tarak karmakar wrote:
Dear Mark,
Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is continuing to increase and not getting equilibrium value. Is that
because my system is not minimized / equilibrated properly ?
Impossible to say... you have to look at the trajectory, and other
observables.
Mark
Any suggestion ?
Thanks
On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
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
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