Cryo_fit1 FAQ

Contents

How long does it take to run cryo_fit?

../images/cryo_fit_FAQ_how_long1.png ../images/cryo_fit_FAQ_how_long2.png

How to enlarge map box size?

How to generate and record movie?

How to improve initial cc?

I see an error message at my 1_make_gro step.

I see "Fatal error: A charge group moved too far between two domain decomposition steps. This usually means that your system is not well equilibrated" at my 8_cryo_fit step.

I see "Fatal error: Number of grid cells is zero. Probably the system and box collapsed." at my 8_cryo_fit step.

I see "step 0 correlation coefficient: nan" at my 8_cryo_fit step.

I see "step 0 correlation coefficient: nan" and "Range checking error: Explanation: During neighbor searching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again." at my 8_cryo_fit step.

I see "User's provided atomic model had 0.0 cc" in my cryo_fit.overall_log.