While a good color scheme will help, the key thing to note here is the need for contrast for enhanced readability. To quote this article from eyemagzine 


  Light grey text on a white background and small text size both lead to
  an increased orbicularis oculi activity and decreased blinking. These
  two conditions are related to text quality, and we would expect to
  find similar indicators of eye fatigue with poor font quality or
  condensed letter spacing.


For examples of good color combinations with sufficient contrast I recommend reading this article on UX matters which has this to say on what contrast to choose for minimal eye strain.


  Ensuring the Readability of Text Through Contrast
  
  For backgrounds behind text, use solid, contrasting colors, and avoid
  the use of textures and patterns, which can make letterforms difficult
  to distinguish or even illegible. Choose combinations of text color
  and background color with care. Value contrast between body text and
  its background color should be a minimum of about eighty percent.
  
  Contrast with a white background
  
  Black text on a white background provides maximal value contrast and,
  therefore, optimal readability for body text. The contrast between
  charcoal gray (#333333) text and a white background is about eighty
  percent—thus giving minimally good value contrast. - 
  
  The following dark colors provide good to excellent contrast and
  legibility for text on a white background: 
  
  


The importance of contrast with regards to reducing eye strain is explained further in the article as highlighted below


  Contrast and Legibility “To provide the best legibility, ensure that text contrasts adequately with its background in both hue and
  value.”
  
  To provide the best legibility, ensure that text contrasts adequately
  with its background in both hue and value. When there is insufficient
  contrast between the hue or value of text and its background color,
  the text appears blurred or has a halo effect around it, making it
  difficult to read and resulting in eye strain.


That said the choice of text and size is also critical. To quote the above referenced eye magazine site article


  Designers usually try to use high quality text when readers are
  expected to read for any period of time, but using a comfortable text
  size is not always possible. In print, there is a trade-off between
  type size and the amount of text that can fit on a page. Nine-point
  type may be chosen because it is cost-effective, whereas eleven-point
  would be easier to identify visually and would reduce eye strain.
  Twelve-point text may be needed for good character definition on
  computer screens, because readers frequently sit further from a screen
  than from a printed page, but many Web pages specify small font sizes
  despite the fact that it costs no more to create additional or longer
  pages. Designers need to argue for larger text sizes to reduce the
  effects of eye strain.


From an Accessiblity standpoint I also recommend looking at W3C guidelines on recommended level of contrast


  1.4.3 Contrast (Minimum): The visual presentation of text and images of text has a contrast ratio of at least 4.5:1, except for the
  following: (Level AA)
  
  
  Large Text: Large-scale text and images of large-scale text have a contrast ratio of at least 3:1;
  Incidental: Text or images of text that are part of an inactive user interface component, that are pure decoration, that are not
  visible to anyone, or that are part of a picture that contains
  significant other visual content, have no contrast requirement.
  Logotypes: Text that is part of a logo or brand name has no minimum contrast requirement.
  


You should also considering offering  a high contrast option which will allow users to work comfortably in low light situations. It would be a good idea to provide multiple options like how kindle handles it as shown below.


With regards the benefits of using the high contrast mode in dark rooms,I recommend looking at this snippet from this article


  However, using light text on a dark background also has its advantages
  for attracting less light in a dark room.


That said, while reversing color ensure this taken care of better readability


  When reversing colour out, eg white text on black, make sure you
  increase the leading, tracking and decrease your font-weight. This
  applies to all widths of Measure. White text on a black background is
  a higher contrast to the opposite, so the letterforms need to be wider
  apart, lighter in weight and have more space between the lines.


Lastly here are some articles on color schemes suitable for coding which might help you make your final decision (I know your application does not deal with users coding on it but the use case is similar here..)

Solarized color schemes help you code longer :To quote the article


  Solarized doesn’t just claim to be easy to read based on the
  designer’s personal preferences, though. Ethan Schoonover, the
  designer responsible for the project, clearly explains the rationale
  behind the decisions he made on the project site. The most prominently
  visible is the use of selective contrast:
  
  “On a sunny summer day I love to read a book outside. Not right in the
  sun; that’s too bright. I’ll hunt for a shady spot under a tree. The
  shaded paper contrasts with the crisp text nicely. If you were to
  actually measure the contrast between the two, you’d find it is much
  lower than black text on a white background (or white on black) on
  your display device of choice. Black text on white from a computer
  display is akin to reading a book in direct sunlight and tires the
  eye. Solarized reduces brightness contrast but, unlike many low
  contrast colorschemes, retains contrasting hues (based on colorwheel
  relations) for syntax highlighting readability.” White-on-black
  themes, popular among developers who want to reduce eye strain, are an
  improvement over black-on-white themes, but the contrast is still far
  too great.


Here are some links worth checking out

Color schemes for vim

What makes a good IDE color scheme

Which color scheme to choose for applications that require long work hours?

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