How does gmx angle calculates angles ? Is there any bug in it ?

01 January 1970 1 9K Report

Hello everyone.

I am having a problem with calculating angle using gmx angle. When I calculated the angles using the command I got certain values. However, using VMD I could see the angles are different from the ones I got using gmx angle. Its not just for a single value. They are different for the entire trajectory. Can anyone explain why its happening ?

Ricardo J Ferreira

Please be aware that atom numbering in VMD starts from 0 (zero), while in gmx angle the first atom is 1 (one). To match VMD with gmx angle it must be (atomnr - 1) in VMD (e.g. if it is 100 in gmx angle, in VMD it should be 99).

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