Re: [gmx-users] genbox box size problem

On 4/29/13 5:30 AM, Alexander Björling wrote: Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased

Re: [gmx-users] genbox box size problem

genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it. You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, mini

[gmx-users] genbox box size problem

Dear users, I am trying to solvate a MARTINI model, using a pre-equilibrated coarse-grained water box. This usually works fine with the following command. genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21 When I recently increased the box size things started going wrong. As the s