Hi, On Thu, Jun 11, 2015 at 1:26 PM 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. > > 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.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. If you want to reply to individual emails, don't subscribe to the list and opt to receive the emails in digest form. > 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 -- 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.