Re: [gmx-users] Which .tpr file to use for g_rms?
On 4/12/2010 6:45 PM, Anirban Ghosh wrote: Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump Did you read trjconv -h about -pbc nojump? Notice how when you didn't give your command lines last time, you didn't get a very useful answer. So which .tpr file should I use? You're trying to measure a membrane thickness. So you want all the membrane residues in the same box, and don't care about anything else. There's various ways to use -pbc and -center to achieve this, depending on what the simulation has done. Mark Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are. Mark Thanks again. Anirban On 12/4/10, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org
Re: [gmx-users] Which .tpr file to use for g_rms?
Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Which .tpr file to use for g_rms?
Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Which .tpr file to use for g_rms?
Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Which .tpr file to use for g_rms?
Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Thanks again. Anirban On 12/4/10, Justin A. Lemkul jalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Which .tpr file to use for g_rms?
On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are. Mark Thanks again. Anirban On 12/4/10, Justin A. Lemkuljalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Which .tpr file to use for g_rms?
Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump So which .tpr file should I use? Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/12/2010 4:33 PM, Anirban Ghosh wrote: Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Since you're not using the coordinates in the .tpr file to extract the last frame and map its coordinates onto the .tpr's atom names, it can't matter what they are. Mark Thanks again. Anirban On 12/4/10, Justin A. Lemkuljalem...@vt.edu wrote: Anirban Ghosh wrote: Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? That's up to you to decide based on what you need to measure. Do you want the RMSD relative to your starting (i.e. crystal/NMR) structure, or are you trying to study how a protein folds, in which case you'd use the native (end) state? like when I an using trjconv to dump my last frame (with -pbc nojump), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? I don't understand what you mean. What has happened is an entire trajectory, not a snapshot. -Justin Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkuljalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Use the one that contains the structure you wish to serve as your reference. -Justin Thanks, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
