I've simulated a mixture of 500 glycine molecules in a ~6.3 nm box, dissolved in water. I looked at the plots for energy and temperature and nothing seems abnormal about them: http://imgur.com/fIdCK0f. However, my radial distribution functions look very wrong: http://imgur.com/J6wN77G. I'm wondering if there is a problem with my input script or if you think I need to double check the parameters for all of my atoms, or if something else might be causing problems. Here's my input script: https://justpaste.it/kei6. I left in my comments - I hope they aren't distracting. I also looked at the movie in vmd, but saw no obvious problems. No atoms were flying around and it didn't look too compressed. I struggled and failed to make a .gif of it though so I can't show that - sorry.
Thanks very much for any help,