> 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 > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@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-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@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.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 > > > > -- > > 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-requ...@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. -- 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-requ...@gromacs.org.