[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Dear GROMACS users and gurus, I am sorry if it's a stupid question...I'm fairly new GROMACS, and something is been driving me crazy. I have a protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces "clustered" compactly for some postproc

Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

sion list for GROMACS users" > Date: Tuesday, December 22, 2009, 7:29 PM > Visvaldas K. wrote: > > Dear GROMACS users and gurus, > > > > I am sorry if it's a stupid question...I'm fairly new > GROMACS, and something is been driving me crazy.  I > have a p

Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

I thought I was sure -pbc cluster will work, but it doesn't :( trjconv get's stuck on an infinite loop while calculating center of mass. In an index.ndx I created a new group which I called CLUSTER, as Mark suggested (I used make_ndx), then I ran trjconv: trjconv -f 1Y2Elig_em.trr -s 1Y2Elig_em