Re: [gmx-users] energy minimization breaks freeze group apart

> Also, I still have an issue with how Gromacs is building my system. when I > run > editconf -f $protName.gro -o box.gro -d 1.2 -bt dodecahedron > Gromacs places the solute in the top corner of the box, rather than > centering it in the box. Shouldn't it be in the center? What am I doing > wron

[gmx-users] energy minimization breaks freeze group apart

My issue : >> I want to do energy minimization on a loop that had been missing and was >> >>filled in by modloop, while freezing the rest of the protein. >> >> Before >> the minimization I have an SO4 ion and 135 water molecules from the >> >>crystallography around the protein. After the minimi

Re: [gmx-users] energy minimization breaks freeze group apart

On Sat, 26 Jan 2008 21:40:20 -0800 Patricia Francis-Lyon <[EMAIL PROTECTED]> wrote: I want to do energy minimization on a loop that had been missing and was filled in by modloop, while freezing the rest of the protein. Before the minimization I have an SO4 ion and 135 water molecules from t

[gmx-users] energy minimization breaks freeze group apart

I want to do energy minimization on a loop that had been missing and was filled in by modloop, while freezing the rest of the protein. Before the minimization I have an SO4 ion and 135 water molecules from the crystallography around the protein. After the minimization the protein has been t