Re: [gmx-users] Minimum distance between periodic images

2013-10-22 Thread Nidhi Katyal
Thank you sir. On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar wrote: > Hi Nidhi, > > These are periodicity artifacts. Make sure that you remove jumps over PBC > from your trajectory by using trjconv -pbc nojump. > > Cheers, > > Tsjerk > > > On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal >wr

Re: [gmx-users] Minimum distance between periodic images

2013-10-22 Thread Tsjerk Wassenaar
Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal wrote: > Dear all users > > I have simulated a protein with two chains (153 residues each) for >

Re: [gmx-users] minimum distance between periodic images does not aggree with box dimensions

2012-05-01 Thread Tsjerk Wassenaar
Hi Thomas, The rhombic dodecahedron is built as a rectangular brick, which makes it easy to fill with a rectangular bricklet of water. Now, for the smaller distances the short edge of the rectangular brick is smaller than the diameter of the particle, and it is represented fragmented. Best way to