[gmx-users] question about the output of minimization

Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # # # # MM# # # # # # # #

Re: [gmx-users] question about the output of minimization

On 7/11/12 6:13 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I did a minimization of my structure. But the output seems a bit strange for me, since my input was the protein with its membrane in a box like this: # = box P = Protein M=Membrane # #

Re: [gmx-users] question about the output of minimization

Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340 4.59470 5.17330 -c -bt dodecahedron -d 1.0 2logErr 1logOut Or

Re: [gmx-users] question about the output of minimization

On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, ah okey. Thank you. And I have another question. Why is the protein in the corner of the box and not in the middle? I thought I centered it with the command: editconf -f wholeProtein.gro -o 3m71_box.gro -center

Re: [gmx-users] question about the output of minimization

Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file. Thank you On 7/11/12 7:12 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Re: [gmx-users] question about the output of minimization

On 7/11/12 7:34 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Yes I tried the command you wrote but it is still in the corner of the box. Is there anything else I can do? The coordinates I used to center the protein are the ones which are in the last line of the .gro file. The