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
