[gmx-users] RMSD plot

[Mark Abraham]

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.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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>