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
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
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
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
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
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