A frame-by-frame comparison of two trajectories might have value for
debugging code, but I'm not sure what the meaning would be otherwise. I
speak from having actually implemented this feature in an old program.
I think you might do better if you can derive clusters of conformations
from each trajectory and comparing those, or just compare minimized
averages of the trajectories if the conformations don't change much.
Bill
On 2/11/16 1:07 AM, Karolina Markowska wrote:
> Dear Amber Users,
>
> I have two simulations with the same system and I would like to compare
> them. Mostly I would like to check if I'm having the same protein
> conformations in these two simulations. Does Amber software provide a tool
> for that kind of analysis?
>
> I wanted to use cpptraj and use the first trajectory as reference, add the
> second one by trajin and calculate rmsd between them, but cpptraj uses only
> the first frame from that file. Can I make cpptraj to read whole trajectory
> as a reference?
> The script looked like that:
>
> parm protein.prmtop
> reference sim1.nc
> trajin sim2.nc
> autoimage
> strip :WAT
> strip :Na+
> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
> quit
>
> | sim1.nc is the trajectory of the first simulation and sim2.nc is the
> trajectory from the second simulation.
>
> Thanks for your help.
> Best regards,
> Karolina Markowska
> PhD student
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Received on Thu Feb 11 2016 - 01:30:04 PST
