[gmx-users] sudden jumps in RMSD etc.

[mu xiaojia]

probably means your trajectory is not continuous enough. I saw the same
thing when I try to "fit" an ensemble trajectory, which each frame is not
from the previous one. Or if your first frame in your trajectory is not
"good looking(or having good rmsd to your target structure)", fit option
cannot fit the rest to such starting structure.

On Thu, Jan 19, 2012 at 4:32 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 20/01/2012 7:55 AM, Yun Shi wrote:
>
>> Hi all,
>>
>> I am doing duplicate MD simulations with a protein-ligand system.
>>
>> After processing one trajectory by trjconv with the optioin -pbc nojump,
>> I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances.
>>
>> Then I tried -pbc mol -ur compact, which did not work. And then -fit
>> progressive on protein atoms, which again did not completely eliminate
>> those jumps in protein atom RMSDs.
>>
>> I wonder if I have not used the right option?
>>
>
> There's a suggested workflow here http://www.gromacs.org/**
> Documentation/Terminology/**Periodic_Boundary_Conditions<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions>which you can adapt to your needs.
>
> Mark
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