PCA plotted for same trajectory using two different software has different sign.

Hi Bio3D,

I generated PCA using Gromacs. Later, I found bio3d package and am impressed by its simplicity and user-friendliness for MD analysis. Therefore, I have started to use it and computed PCA. After projecting the snapshots into PCA subspace, I found the difference. First five snapshots are shown as an example. A trend is similar for entire trajectory.

GROMACS generated projection (nm) SN PC1 PC2 1 2.01515 0.15200 2 2.89946 -1.34934 3 1.87425 0.23617 4 1.63961 0.76003 5 0.90918 2.17062

Bio3D generated projection ,V1,V2,V3 1,-20.1535551535521,-1.53137220354993 2,-28.9957972175446,13.4866462107036 3,-18.7430155734459,-2.37174087332255 4,-16.3898777344419,-7.61623760143872 5,-9.08356004683468,-21.7176721873223

By looking at the first row generated by both methods, I can see the difference. First, one order of magnitude difference is due to the unit (nm vs angstrom). Second, minus in a projection by one method has plus by another method. I got confused and wondering whether there is something wrong.

Does somebody have any explanation on it?

Thank you in advance.

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