> From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 134, Issue 66
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Date: Thu, 11 Jun 2015 11:37:49 +0200
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> 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.bih...@outlook.com>
> To: GROMACS users mailing list <gmx-us...@gromacs.org>
> Subject: [gmx-users] Clustering energy minimized equally space frames
> Message-ID: <blu185-w18f55caf878865ffc45492ff...@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.abra...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Clustering energy minimized equally space
> frames
> Message-ID:
> <CAMNuMAS0q8R6a9pwKBCt+UCcRbTY-=7ngm_wjopojn-o0mc...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Thu, Jun 11, 2015 at 9:00 AM ashish bihani <ashish.bih...@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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#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.
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