Re: [gmx-users] Imaging in PBC simulations -summary

Dear Jochen and Tamas, thanks for your replies. I tried both, the trjconv -fit postprocessing and setting comm_mode for mdrun and actually only the latter worked fine. In the former, protein drifts toward the box side and jumps out for some frames, leaving its bound ions inside the box. Better

[gmx-users] Imaging in PBC simulations

Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a starting gro and than

Re: [gmx-users] Imaging in PBC simulations

I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.On 4/24/06, Martin LEPSIK [EMAIL PROTECTED] wrote:Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best wayto image a

Re: [gmx-users] Imaging in PBC simulations

Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a

Re: [gmx-users] Imaging in PBC simulations

Martin LEPSIK wrote: Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best way to image a protein with a ligand inside a triclinic water box? I run an MD in GMX-3.3 with nstcomm=1, comm_grps and comm_mode not set. I watch the movie in VMD, loading first a