[gmx-users] RMSD plot

tarak karmakar tarak20489 at gmail.com
Mon Jul 30 08:49:11 CEST 2012

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 ?
Any suggestion ?


On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham <Mark.Abraham at 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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