Oh, I see I forgot to state that X should be set to the trajectory name: X=/some/where/trajectory.xtc python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc
or just python -c 'X=open("/some/where/trajectory.xtc").read(); print X[X.rfind(X[:8]):]' > last.xtc Cheers, Tsjerk On Fri, Nov 25, 2011 at 10:01 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey, > > You don't actually need to copy the trajectory. trjconv and other > tools are comfortable operating on an unfinished trajectory. They'll > just bail out at the end. As an alternative, here's a python one-liner > to extract the last frame (along with unfinished frames) from an XTC > trajectory: > > python -c 'X=open("'$X'").read(); print X[X.rfind(X[:8]):]' > last.xtc > > It will read in the whole trajectory in memory, so better not do it > with very large files ;) > > Cheers, > > Tsjerk > > On Fri, Nov 25, 2011 at 9:08 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: >> On 25/11/2011 6:53 PM, James Starlight wrote: >> >> This way I've already used but is this possible to extract Gro and trp files >> from uncompleated runs and not stopping this simulation ? >> >> Copy the trajectory file. Then use trjconv on the copy however suits you. >> You don't need a new .tpr, you need either the original .tpr or one that >> suits your analysis. >> >> Mark >> >> >> >> James >> >> 2011/11/25 Mark Abraham <mark.abra...@anu.edu.au> >>> >>> On 25/11/2011 6:38 PM, James Starlight wrote: >>> >>> Mark, Tsjerk thanks! >>> >>> I've check my uncompleated produced MD run by G_energy and find that >>> average pressure is 1.1 Bar that is most close to ref. >>> >>> >>> By the way could you tell me about extra possible ways of checking running >>> simmulation? ( E.g I'm calculating long produce trajectory and want to check >>> my uncompleated system ). >>> >>> As I understood One of the possible way is the ussage of G_energy but how >>> I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr) >>> (recently I've asked about this but I've missed that topic ;o) ? >>> >>> Choose a length of time in advance that you are happy to risk being >>> wasted. Run that length of time, make a backup, check whatever you want to >>> check, then continue the simulation. As you acquire confidence, you will >>> want to increase that time (and like everyone you will regret that decision >>> at least once!) >>> >>> Mark >>> >>> >>> >>> >>> Thanks again >>> >>> James >>> >>> 2011/11/25 Tsjerk Wassenaar <tsje...@gmail.com> >>>> >>>> Hi James, >>>> >>>> There have been extensive discussions about this on the list. Check the >>>> archives. In short, smaller systems give larger fluctuations, and shorter >>>> simulations give larger deviations from the expected average. >>>> >>>> Cheers, >>>> >>>> Tsjerk >>>> >>>> On Nov 25, 2011 7:23 AM, "James Starlight" <jmsstarli...@gmail.com> >>>> wrote: >>>> >>>> Dear Gromacs Users! >>>> >>>> >>>> At the present time I'm simulating small peptide (11 a.c in coiled >>>> conformation) in water. >>>> >>>> I've desided to use parameters from Lysozyme simmulation ( opls ff for >>>> parametrisation and all mdp parameters from that simulation). >>>> >>>> Because my peptide was smaller than typical globular protein I've desided >>>> to use bigger periodical box than in tutorial >>>> >>>> I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial >>>> wich resulted in bigger box relative peptide size. >>>> >>>> so i have this box vectors 5.39318 5.39318 5.39318 >>>> >>>> My experiment was in full agreement with the above tutorial until NVP >>>> phase was conducted. I have conducted 100ps equilibration but When I've >>>> checked average pressure it was 0.75 atm instead of 1 BAR and have big >>>> RMSD- >>>> 200. (also I've checked my system visually but it looks fine- I have not >>>> pointed any artifacts linked with unstable pressure like voids in the >>>> solvent etc). Should I equilibrate my sustem longer until pressure would >>>> not >>>> be stabilized to reference BAR? What another options should i take into >>>> account during simulation of the small peptides ? >>>> >>>> Thanks, >>>> >>>> James >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists