in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 10000 ps, therefore in total 1001 frames.
I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file trj.xtc. trr Many thanks! Anna >----Messaggio originale---- >Da: ckut...@gwdg.de >Data: 24/07/2013 13.09 >A: "battis...@libero.it"<battis...@libero.it>, "Discussion list for GROMACS users"<gmx-users@gromacs.org> >Ogg: Re: [gmx-users] Rotation Constraints - PMF + rerun > >On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote: > >> Dear Carsten, >> >> Thank you very much for your very useful help! >> I'm making some tries to test the orire options that probably will solve my >> problem. >> >> In order to do not waste resource, I thought using the rerun option of mdrun I >> can use the trajectories generated before, where my mistake was to allow the >> rotation of my structure. >> So I generated a new topol.tpr file changing the orire options in the mdp and >> I made: >> >> 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr >> 2. trjcat -f traj.trr -o trajout.xtc >> >> but in the trajout.xtc there is only one point as I can check for example >Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr >to trigger output of all .xtc frames. How many frames are in ../traj.xtc? > >Carsten > >> with: >> 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx >> >> >> Could you confirm me that it is not possible follow this idea? >> In fact I suppose that this method it is not applicable; but it is necessary >> to generate a new trajectory, because the angular restraints modify completely >> the trajectory. >> >> Or, just to be sure, did I not made the things in the right way? >> >> Thank you very much! >> >> Anna >> >> >>> ----Messaggio originale---- >>> Da: ckut...@gwdg.de >>> Data: 23/07/2013 13.09 >>> A: "battis...@libero.it"<battis...@libero.it>, "Discussion list for GROMACS >> users"<gmx-users@gromacs.org> >>> Ogg: Re: [gmx-users] Rotation Constraints - PMF >>> >>> Hi Anna, >>> >>> please have a look at the Enforced Rotation Section in the Gromacs 4.6 >> manual. >>> You can restrain the angle of rotation about an axis by setting the rotation >> rate >>> to zero. There is also a 4.5 add-on available with rotational restraints in >>> the Gromacs git repository (branch "rotation"). For more info you may want to >>> look at this page: >>> >>> http://www.mpibpc.mpg.de/grubmueller/rotation >>> >>> Best, >>> Carsten >>> >>> >>> On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: >>> >>>> Dear user and expert, >>>> I'd like ask you a suggestion about a problem that I will try present you >> schematically. >>>> I have got a structure "s" and I have generated the topolgy file itp for it. >> A number of separate "s" in turn generate a complex structure A, that is >> characterized by a cylindrical shape. >>>> Now, I constructed a system with two cylindrical structures, A and B (in >> total made by 64 "s" structures), and I'd like make an Umbrella Sampling >> calculation in order to study the PMF varying the distance between A and B. >>>> >>>> My problem is that I'd like fix the orientation of the axis of each >> structure A and B long the z axis, during the dynamics. >>>> So I need to put a force into the system or a constrain, such that when the >> axis of A or B rotates respect to z axis, the force puts back the axis of the >> structure in the z direction. >>>> >>>> It this possible? If it is so, could you tell me how to do that? >>>> Than you very much, >>>> Anna >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> >>> -- >>> Dr. Carsten Kutzner >>> Max Planck Institute for Biophysical Chemistry >>> Theoretical and Computational Biophysics >>> Am Fassberg 11, 37077 Goettingen, Germany >>> Tel. +49-551-2012313, Fax: +49-551-2012302 >>> http://www.mpibpc.mpg.de/grubmueller/kutzner >>> http://www.mpibpc.mpg.de/grubmueller/sppexa >>> >>> >> >> >> -- >> 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 > > >-- >Dr. Carsten Kutzner >Max Planck Institute for Biophysical Chemistry >Theoretical and Computational Biophysics >Am Fassberg 11, 37077 Goettingen, Germany >Tel. +49-551-2012313, Fax: +49-551-2012302 >http://www.mpibpc.mpg.de/grubmueller/kutzner >http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- 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
