[gmx-users] Clustering energy minimized equally space frames

[Mark Abraham]

Hi,

On Thu, Jun 11, 2015 at 9:00 AM ashish bihani <ashish.bihani at outlook.com>
wrote:

>
>
>
> I extracted [was instructed to extract] trajectory frames at every 10 ps
> from a 10ns xtc file and energy minimized each of them. How do I cluster
> them?
> I tried to do "ls *.gro | gmx cluster -f {.}.gro ", did not work.
>

Unfortunately, the description "did not work" doesn't let us help you fix
it.


> I concatenated the frames and made an xtc file and tried to cluster it in
> MSMbuilder which did not work. Clustering it in gmx cluster would require a
> tpr file which is not there for this trajectory. What do I do?
>

Since you later need a .tpr file for the EM, there's no additional problem.
If you don't have access to (making) the original .tpr that made the
simulation, how can anybody reproduce this work?

Mark


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