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

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

Search: trjconv pbc cluster on the gromacs mailing list and take a look at the first hit. Basically, you need to find a frame that *does* work with -pbc cluster and then make a new .tpr based on the clustered .gro and then run trjconv -pbc mol. Just ensure that this frame is as close to the

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

Thank you, Mark, for your tip, the indexing solution is perfect! Regards, Vis --- On Tue, 12/22/09, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB?

[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

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

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 protein, two metal ions, and inhibitor in my system. Somehow in some of the frames I can't keep all those pieces clustered