[gmx-users] Clustering energy minimized equally space frames

[ashish bihani]

> From: gromacs.org_gmx-users-request at maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 134, Issue 66
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Date: Thu, 11 Jun 2015 11:37:49 +0200
> 
> Send gromacs.org_gmx-users mailing list submissions to
> 	gromacs.org_gmx-users at maillist.sys.kth.se
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> 	gromacs.org_gmx-users-request at maillist.sys.kth.se
> 
> You can reach the person managing the list at
> 	gromacs.org_gmx-users-owner at maillist.sys.kth.se
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Clustering energy minimized equally space frames (ashish bihani)
>    2. Re: Clustering energy minimized equally space frames
>       (Mark Abraham)
>    3. energy groups definition (gozde ergin)
>    4. problem using grompp (Sotirios Dionysios I. Papadatos)
>    5. Re: energy groups definition (gozde ergin)
>    6. Crash of DD with periodic_molecules (Semen)
>    7. Re: problem using grompp (Mark Abraham)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 11 Jun 2015 12:29:48 +0530
> From: ashish bihani <ashish.bihani at outlook.com>
> To: GROMACS users mailing list <gmx-users at gromacs.org>
> Subject: [gmx-users] Clustering energy minimized equally space frames
> Message-ID: <BLU185-W18F55CAF878865FFC45492FFBC0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> 
> 
> 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?
> 
>  		 	   		  
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 11 Jun 2015 07:54:58 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Clustering energy minimized equally space
> 	frames
> Message-ID:
> 	<CAMNuMAS0q8R6a9pwKBCt+UCcRbTY-=7nGm_wjOPOJn-o0MC-DA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> 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
> 
> 
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.

#Okay, sorry about that. 
#I can't understand how you reply to one particular thread in a mailing list. 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.

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. 
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?
2. Is there any alternative to cluster so many .gro files?

#Thanks in advance and sorry about the inconvenience.