Carlos:
Thanks for the quick reply, I checked the RMSD for each monomer and it shows five of them reach plateau at ~3ns and two of them have second plateau at ~13ns. So the problem might not be the relative motion but the different conformation sampled by each monomer. It is strange and very interesting since it is homo-octomer protein and the coordinate are generated from symmetry operation.
I think the lesson here is RMSD is not the only criteria to determine the stability of MD. Previously I always thought that a plateau should be formed if an equilibrium is reached. I guess that's the case for small protein and not for big complex in the limited simulation time. the trajectory will be useful if unusual RMSD could be rationalized.
Let me know if you have more comments. Thanks again for your help. Quoting Carlos Simmerling
<carlos.simmerling.gmail.com>:
> try calculating the rmsd of each monomer individually. it's not
> unusual for multimers to have slow motions relative to each other.
>
> On Sun, Jan 10, 2010 at 3:34 PM, <luzhenw1.msu.edu> wrote:
>> Dear amber community:
>>
>> I have run a 20ns simulation for an octomer protein. The trajectory
>> seems OK after visually check in VMD. However, the RMSD vs time plot
>> shows an continuous increased pattern(see attachment) although the
>> range is small, (from 1 to 1.5 Angstrom). It seems to me that a
>> plateau should be reached after equilibration. on the other hand, I
>> think 20ns is long enough for the system to reach equilibrium. here
>> is my question:
>>
>> Is this an indication of somethin wrong with the simulation? what
>> might be the reason? IF it is normal, What kind of analysis could be
>> used to figure out the origin of RMSD increase?
>>
>> Your kind of help will be very appreciated. Let me know if further
>> information will help.
>>
>>
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Received on Sun Jan 10 2010 - 19:30:02 PST
