[gmx-users] Re: MSD and frequency of writing trajectories
Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Thank you so much! Shirley On May 22, 2013, at 10:31 AM, gmx-users-requ...@gromacs.org wrote: Re: MSD and frequency of writing trajectories -- 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] Re: MSD and frequency of writing trajectories
On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- 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] Re: MSD and frequency of writing trajectories
Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Re: MSD and frequency of writing trajectories
Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
Re: [gmx-users] Re: MSD and frequency of writing trajectories
Thanks for the reply, trjconv does not have any bugs in removing pbc, right? We can just feed the -nojump output to g_msd. I am going to output the coordinates and velocities with g_traj and run it through my own code :) On Wed, May 22, 2013 at 11:19 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Re: MSD and frequency of writing trajectories
On Wed, May 22, 2013 at 8:05 PM, rajat desikan rajatdesi...@gmail.comwrote: Thanks for the reply, trjconv does not have any bugs in removing pbc, right? We can just feed the -nojump output to g_msd. Maybe. There are not (yet) any automated tests for the code in these tools. But probably trjconv -nojump works correctly else we'd have heard more screaming... Mark I am going to output the coordinates and velocities with g_traj and run it through my own code :) On Wed, May 22, 2013 at 11:19 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
