Re: [gmx-users] restore pbc after a rotation

2009-01-27 Thread XAvier Periole
Hi Tsjerk, There is no rush and I really can use the copies of the box. But as you insist I'll send you the gro file off list. XAvier. On Jan 26, 2009, at 9:06 PM, Tsjerk Wassenaar wrote: Hi Xavier, By when do you need it? You can send me one frame ( .gro) and I can see what I can do. But

Re: [gmx-users] restore pbc after a rotation

2009-01-26 Thread Tsjerk Wassenaar
Hi Xavier, By when do you need it? You can send me one frame ( .gro) and I can see what I can do. But no guarantees, and no time indication :( Cheers, Tsjerk On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole wrote: > > On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote: > >> Hi XAvier, >> >> U

Re: [gmx-users] restore pbc after a rotation

2009-01-26 Thread XAvier Periole
On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote: Hi XAvier, Unfortunately, you're out of luck. The coordinates do not contain information regarding the proper orientation with respect to the coordinate system. No they don't. May be I should have mentioned that I know for each conformati

Re: [gmx-users] restore pbc after a rotation

2009-01-26 Thread Tsjerk Wassenaar
Hi XAvier, Unfortunately, you're out of luck. The coordinates do not contain information regarding the proper orientation with respect to the coordinate system. That's the short answer. I guess you did save all atoms, at least of proteins and lipids, in which case you could do a search for a rota

[gmx-users] restore pbc after a rotation

2009-01-25 Thread XAvier Periole
Dears, I need to rerun a trajectory that has been rotated to orient a molecule according to a reference. The pbc are therefore broken. Would anyone know how to restore the correct position of the atoms inside the unit cell after the rotation is applied. The rotation is actually applied arou