Re: [gmx-users] Potential energy of protein after energy minimization

Hello Sir I have generated the structure using PHYRE server, performed its structural validations. As per your suggestion I have checked the protein in both visualizing software. During MD simulation of the protein, the pdb2gmx is generating topol.top and .itp without any errors. Do I need to

[gmx-users] Potential energy of protein after energy minimization

Hii I am simulating protein (PfCDPK5) in water. After performing energy minimization, the potential energy of my protein is 2.86082e+07. As mentioned in the tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html, the Epot should be negative. The