Re: [gmx-users] trjconv correct the pbc before analysis

Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. But if one want to extract such coordinates out for computing it myself, it is

Re: [gmx-users] trjconv correct the pbc before analysis

On 4/05/2012 4:03 AM, mu xiaojia wrote: Thanks Justin and Mark, I compared g_rama's results for no pbc treated trajectory and pbc treated trajectory, it seems they are the same. So gromacs' analysis tools know how to deal with the broken molecules. Caveat: some tools seem to be better than

[gmx-users] trjconv correct the pbc before analysis

Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may appear to jump across to the other side

Re: [gmx-users] trjconv correct the pbc before analysis

On 5/2/12 8:55 PM, mu xiaojia wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will diffuse through the unit cell, and may

Re: [gmx-users] trjconv correct the pbc before analysis

On 03/05/12, mu xiaojia muxiaojia2...@gmail.com wrote: Dear gmx users, I have a question about using the trjconv -pbc options before analyzing my trajectory. It's stated by Justin's tutorial that: use trjconv to account for any periodicity in the system. The protein will