Re: [gmx-users] Removing Water from Final Simulation
... and see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volumefor prevention cure. Mark On Mon, Jun 3, 2013 at 3:47 AM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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 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] Removing Water from Final Simulation
Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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] Removing Water from Final Simulation
trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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] Removing Water from Final Simulation
Thanks Warren for your help, those were exactly the functions I was looking for! However I'm still experiencing a bit of trouble because my simulated protein contained a heme cofactor and it seems to only let me extract one object. Have you had any experience with this? Parker On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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 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] Removing Water from Final Simulation
What group did you select from the list offered when you ran the script? Did it include all of your molecules, minus water? Or did you just select something like Protein? You need to run make_ndx and general a group that contains all of the molecules you want. So you will want to do something like 1 | 2 | 3 when running make_ndx What those numbers are depends on what is contained within the gro file you feed it. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Removing Water from Final Simulation Thanks Warren for your help, those were exactly the functions I was looking for! However I'm still experiencing a bit of trouble because my simulated protein contained a heme cofactor and it seems to only let me extract one object. Have you had any experience with this? Parker On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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 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] Removing Water from Final Simulation
FYI you can also take the complement of an existing group with make_ndx using the ! symbol. e.g. if water is group 0, you could make a group of everything but water using: !0 This might be easier/more foolproof than concatenating all other groups when generating the appropriate index file as suggested in the previous email. Best, - Reid On Sun, Jun 2, 2013 at 10:40 PM, Dallas Warren dallas.war...@monash.eduwrote: What group did you select from the list offered when you ran the script? Did it include all of your molecules, minus water? Or did you just select something like Protein? You need to run make_ndx and general a group that contains all of the molecules you want. So you will want to do something like 1 | 2 | 3 when running make_ndx What those numbers are depends on what is contained within the gro file you feed it. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Removing Water from Final Simulation Thanks Warren for your help, those were exactly the functions I was looking for! However I'm still experiencing a bit of trouble because my simulated protein contained a heme cofactor and it seems to only let me extract one object. Have you had any experience with this? Parker On Sun, Jun 2, 2013 at 9:47 PM, Dallas Warren dallas.war...@monash.eduwrote: trjconv for trajectories editconf for coordinate files Along with an appropriately generated index file (using make_ndx) which contains the molecules you want in the output within a single group. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Parker de Waal Sent: Monday, 3 June 2013 11:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Removing Water from Final Simulation Hi GMX users! I just completed my first 30 ns simulation and would to remove all water molecules from the resulting .gro and trajectory files for the sake of my HDD. Does anyone know how to do this? Cheers, Parker -- 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 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 -- Reid Van Lehn NSF/MIT Presidential Fellow Alfredo Alexander-Katz Research Group Ph.D Candidate - Materials Science -- 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
