R: Re: [gmx-users] Rotation Constraints - PMF + rerun
in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 1 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", "Discussion list for GROMACS users" >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", "Discussion list for GROMACS >> users" >>> 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 listgmx-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&#
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", "Discussion list for GROMACS > users" >> 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 listgmx-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 listgmx-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 listgmx-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
R: Re: [gmx-users] Rotation Constraints - PMF + rerun
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 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", "Discussion list for GROMACS users" >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 listgmx-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 listgmx-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
