How to read large dcd files; change X-axis to Time (ns); plot secondary structure throughout simulation; plot free energy landscape?

[Former user]

Dear all,

I have read previous issues related to my problems but I cannot figure out the answers. I am a novice in R and also in programming. My operating system is Mac Mojave. I have four questions and they are all related to bio3d. They are as follows-

1. I am trying to read a large dcd file (over 5GB) and i am getting an error saying "Vector Memory Exhausted". So to solve this problem should i break the dcd files into smaller parts? If i do so then how can i plot the results together for all the time-frame together?

2. Secondly, i would also like to know if i can plot the X-axis with "Time-interval (ns or ps)" rather than "No. of Frames" as shown in Fig 1. In order to do so what should i do?

3. Is there any way to plot secondary structure changes throughout the simulation as shown in Fig 2? If yes, then how could i do that?

4. Is there any way to plot free energy landscape as shown in Fig 3?

I have already spent over 1 month trying to fix these issues, and so finally i am posting my questions here. Any help would be much appreciated! Thank you for your time.

With kind regards Amit

[mike jachem]

I can try to help you tackle question one. Load your psf and dcd in VMD and save the dcd with a bigger stride (say 500) by default it is one. Then load it back to bio3d. Memory is a really big issue in bio3d!!

[Xinqiu Yao]

Thanks for answering the question, Mike. We are working to solve the memory issue.

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The questions 2-4 are all related to R basic plotting functions and you may get quicker answers from other places such as StackOverflow. Note that we have limited time and energy to maintain this issue tracker and may not response promptly to non-bio3d related questions.