[gmx-users] Clustering energy minimized equally space frames

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 11 13:38:02 CEST 2015


Hi,

On Thu, Jun 11, 2015 at 1:26 PM 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.
> > 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?
> >
> >
> >
> > 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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> > >
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>
> #Okay, sorry about that.
> #I can't understand how you reply to one particular thread in a mailing
> list.


If you want to reply to individual emails, don't subscribe to the list and
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> Please see if I am doing this correctly this time.
> #I have solved my problem. It was a bit bizarre, so here is a summary:
>
> I ran a 10 ns MD simulation (mdrun) and created a .gro file (trjconv)
> every 10 ps. I minimized (mdrun) each of these files. I needed to cluster
> these so that I could look at representative structures from the simulation
> of the intermediate.
>
> Now,
>
> 1.
> "gmx cluster -f *.gro -s run.tpr <<<0" or "ls *.gro | gmx cluster -f
> {.}.gro -s run.tpr <<<0" just reads the first .gro file out of the
> directory that contains all the frames and stops. It lists all the
> filenames that ls fed to it. Because -f takes only one argument here.
>

Right, like gmx cluster -h suggests.


> 2.
> I concatenated all these .gro files(trjcat). The .xtc file thus created
> has frames that don't really have anything to do with each other.
>

That's fine. It's a container data format. Whether there's a conceptual
relationship is for you to manage.

I did not know that I could use the same .tpr file (for gmx cluster) that I
> had prepared with grompp before mdrun. I used that and it worked. I
> clustered the frames with monte-carlo.
>
> So, I have two questions:
> 1. The monte-carlo clsutering method does not mention a cluster centre in
> cluster.log. How do I get that?


I would read about this method in gmx cluster -h before using it, decide it
wasn't a clustering method, and choose something else.

Mark


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