I am relatively new with computational methods, so any help is appreciated. When i try to open up a prmtop file and an mdcrd file to analyze a MD simulation in water (after I have aligned the mdcrd file), the image looks very distorted, like most of the bond lengths are unreasonable. I loaded the mdcrd file with a periodic box. I've included a picture. What causes this and how can it be fixed?
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Received on Fri Dec 28 2012 - 11:00:03 PST
