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

2012-05-03 Thread Mark Abraham
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

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

2012-05-03 Thread mu xiaojia
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 necessa

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

2012-05-02 Thread Mark Abraham
On 03/05/12, 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 th

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

2012-05-02 Thread Justin A. Lemkul
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

[gmx-users] trjconv correct the pbc before analysis

2012-05-02 Thread mu xiaojia
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 sid