[gmx-users] Free energy landscpae

[Sun Iba]

Hello users and experts
I have performed a protein-ligand simulation with Gromos 43a1 ff and SPC
water model. I performed PCA and selected first 2 principal components for
construction of FEL using gmx sham. However, from the available references
i have seen that the there exist both positive and negative values on FEL
X- and Y-axis around a central 0 value. But in my case, the most populated
region lies far away from 0, i.e. towards "negative" values of PC1
(starting from -2.5 to 0.0; there are no positive values after 0.0) .
Please have a look at this image and suggest why is it so.

https://drive.google.com/drive/my-drive

With Regards