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 <[email protected]>wrote: > 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 > [email protected] > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > -----Original Message----- > > From: [email protected] [mailto:gmx-users- > > [email protected]] 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 > > <[email protected]>wrote: > > > > > 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 > > > [email protected] > > > +61 3 9903 9304 > > > --------------------------------- > > > When the only tool you own is a hammer, every problem begins to > > resemble a > > > nail. > > > > > > > > > > -----Original Message----- > > > > From: [email protected] [mailto:gmx-users- > > > > [email protected]] On Behalf Of Parker de Waal > > > > Sent: Monday, 3 June 2013 11:10 AM > > > > To: [email protected] > > > > 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 list [email protected] > > > > 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 [email protected]. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > > > gmx-users mailing list [email protected] > > > 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 [email protected]. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * 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 list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
