RE: [gmx-users] editconf and g_rmsdist

2009-09-24 Thread Enemark Soeren
Sent: Friday, September 18, 2009 7:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] editconf and g_rmsdist Hi Soren, >  Why I am seeing this difference? Is it due to round-off's after the > transformation to center the molecule in the box? Or am I using g_rmsdist >

Re: [gmx-users] editconf and g_rmsdist

2009-09-18 Thread Tsjerk Wassenaar
Hi Soren, >  Why I am seeing this difference? Is it due to round-off’s after the > transformation to center the molecule in the box? Or am I using g_rmsdist > wrongly? It's a bit weird indeed. You might be right that it's due to round-off errors. You can try to copy the original gro file and repl

[gmx-users] editconf and g_rmsdist

2009-09-18 Thread Enemark Soeren
Dear GMX-users I have a question about what happens when editconf is used to "box" a molecule. The reason I ask is because, I have used g_rmsdist in order to study how a very small piece of a structure (100+ atoms) relaxes towards its native state (given by NMR) after a small perturbation.