How to change no. of frames

[Gagan Jyot]

Hii ,

I am using carma for network analysis. I have a trajectory of 5000 frames, but carma is using only 10 frames for the analysis. I want it to use atleast 10% frames.

Is there any way to make changes in the calculation ?

Thanks in advance,

Gagan 

[Nicholas Glykos]

Hi, 

Not enough info. I do not understand which analysis you refer to (given that carma does not do network analysis). Either show the carma command line you are using, or explain for which part of your calculations you use carma. 

NMG

[Gagan Jyot]

I am performing dynamic network analysis. The tutorial i am following is : https://luthey-schulten.chemistry.illinois.edu//tutorials/network/network_tutorial.pdf

This uses carma to calculate covariance and correlation. VMD automatically calls the program and do the calculations. Here, it takes only 10 frames for the analysis irrespective of how many frames are there in the trajectory.

Thanks for your response.

Gagan

[Nicholas Glykos]

OK. This is not a carma issue. Carma will use all frames that it is asked to use. The '10 frames' you are seeing are not selected by carma, probably VMD passes arguments that restrict the number of frames. Let me say the same thing differently. If you say, for example, something like :

carma -v -w -col -cov -dot -super -atmid HEAVY  MY.dcd  MY.psf

you will see that carma will use all frames that are present in MY.dcd

[Gagan Jyot]

Okk. I got that. Thank you for the prompt response.

How can I solve this problem now? If u can help!

Thanks,

Gagan

[Nicholas Glykos]

I do not have practical experience from the analysis you are doing. I would try to locate at which of the previous steps of the analysis only 10 frames were selected. Bear in mind that what you see may be the 'correct' procedure given that you only have 5000 frames.