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

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

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 >

[gmx-users] Minimum distance between periodic images

Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for f

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

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

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

Dear GROMACS users, I have a nanoparticle (perfect sphere) and want to enclose it into a rhombic dodecahedron. For this purpose I use the following command lines editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o nano_box_EM