Issue with H-Bond Calculation

[NN]

Dear Professor, 

Thank you very much for providing this excellent program for hydrogen-bond calculations.

I recently encountered an issue while using the program. When I run the following command:

hbc a.gro b.xtc z 0 -1 1 {{0 0 28} {25 43 62} {1 1 17}} {resname SOL} 3.5 40.0 1

the calculation works as expected. However, when I change the z-range from 28–62 to 29–63, using:

hbc a.gro b.xtc z 0 -1 1 {{0 0 29} {25 43 63} {1 1 17}} {resname SOL} 3.5 40.0 1

all of the output values become zero.

I was wondering what might be causing this behavior and whether there is a way to resolve the problem. Any guidance would be greatly appreciated.

Thank you for your time and assistance.

[Y. Wang]

Hi,

This error looks very strange to me as well. First, please check if you strictly use the command format, sometimes small format errors may lead to unexpected output without throwing an error or warning in tkconsole; then have you visually checked your cell dimensions, especially in Z direction? Can you try to do the calculations on only one frame (such as one .gro file)? If error persists, do you mind sending me this .gro file, I will have a look. You can send it to my private email yuxiang...@gmail.com.

Best regards,

Yuxiang

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