Re: [gmx-users] Problem with minimizing the energy of the solvated system

On 7/5/12 3:15 PM, jonas87 wrote: Chopping out a bunch of unnecessary stuff... *editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d 1.0 * Read 1202 atoms No velocities found system size : 5.245 4.320 2.507 (nm) diameter: 5.532 (nm) ce

[gmx-users] Problem with minimizing the energy of the solvated system

Hi, I'm new to gromacs, after following a few lectures on MD decided to try out this gromacs tutorial: http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html I can get till the section "Energy minimization of the solvated system" but then I get a