Re: [gmx-users] trjcat after trjconv
Thank you sir. On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar wrote: > Yes. > > Cheers, > > Tsjerk > > > On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote: > > > Thanks for the quick reply sir. > > So, does it mean I can apply "trjcat" on the processed xtc files??? > > > > > > On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar > >wrote: > > > > > Hi Venkat, > > > > > > These options are 'frame intrinsic' or 'history independent', unlike > -pbc > > > nojump. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > > > > > Dear Tsjerk sir, > > > I used trjconv -pbc mol -ur compact options. > > > > > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > > > wrote: > Hi Venkat, > > It... > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/g... > > > -- > > > 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 > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
Re: [gmx-users] trjcat after trjconv
Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote: > Thanks for the quick reply sir. > So, does it mean I can apply "trjcat" on the processed xtc files??? > > > On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar >wrote: > > > Hi Venkat, > > > > These options are 'frame intrinsic' or 'history independent', unlike -pbc > > nojump. > > > > Cheers, > > > > Tsjerk > > > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > > > Dear Tsjerk sir, > > I used trjconv -pbc mol -ur compact options. > > > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > > wrote: > Hi Venkat, > > It... > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/g... > > -- > > 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 > > > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] trjcat after trjconv
Thanks for the quick reply sir. So, does it mean I can apply "trjcat" on the processed xtc files??? On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > These options are 'frame intrinsic' or 'history independent', unlike -pbc > nojump. > > Cheers, > > Tsjerk > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > Dear Tsjerk sir, > I used trjconv -pbc mol -ur compact options. > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > wrote: > Hi Venkat, > > It... > > > -- > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/g... > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
Re: [gmx-users] trjcat after trjconv
Hi Venkat, These options are 'frame intrinsic' or 'history independent', unlike -pbc nojump. Cheers, Tsjerk On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > It... > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/g... -- 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
Re: [gmx-users] trjcat after trjconv
Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > It depends on what you mean with "removing pbc". > > Cheers, > > Tsjerk > > On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: > > Dear Sir, > Thanks for the quick reply. > I accidentally lost one of my raw .xtc files. But I have the noPBC xtc > file. So, when ever I extend my simulation, first I am removing PBC then > concatenating it with existing noPBC xtc file. Is it fine?? > > > On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban >wrote: > > > I do not think that I ever tried myself, but is seems all the same. > Why > do you ask? > > > Dr. V... > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
Re: [gmx-users] trjcat after trjconv
Hi Venkat, It depends on what you mean with "removing pbc". Cheers, Tsjerk On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removing PBC then concatenating it with existing noPBC xtc file. Is it fine?? On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrote: > I do not think that I ever tried myself, but is seems all the same. > Why do you ask? > > > Dr. V... -- 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
Re: [gmx-users] trjcat after trjconv
Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removing PBC then concatenating it with existing noPBC xtc file. Is it fine?? On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrote: > I do not think that I ever tried myself, but is seems all the same. > Why do you ask? > > > Dr. Vitaly V. Chaban > > > On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote: > > Dear all, > > I have a basic doubt. Is there any difference between the two processes > > where > > 1) I concatenate the trajectories and do trjconv to remove PBC, which is > a > > default process > > 2) Do trjconv on all the xtc files separately and then concatenate them. > > > > Thank you for your time > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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 > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
Re: [gmx-users] trjcat after trjconv
I do not think that I ever tried myself, but is seems all the same. Why do you ask? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote: > Dear all, > I have a basic doubt. Is there any difference between the two processes > where > 1) I concatenate the trajectories and do trjconv to remove PBC, which is a > default process > 2) Do trjconv on all the xtc files separately and then concatenate them. > > Thank you for your time > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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 -- 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
[gmx-users] trjcat after trjconv
Dear all, I have a basic doubt. Is there any difference between the two processes where 1) I concatenate the trajectories and do trjconv to remove PBC, which is a default process 2) Do trjconv on all the xtc files separately and then concatenate them. Thank you for your time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
