Re: [gmx-users] can dynamic selection be used with gmx rdf?
Here I am posting the solution of the problem that I described in my first post: gmx rdf -f ../../../../traj_200to500.xtc -s ../../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref '(resname DPPS and name O22) and within 0.3 of name CAL' -sel 'name OH2' Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cardenas, Alfredo E Sent: Thursday, February 28, 2019 10:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi Mark, Thanks for your reply. I have tried the following run: gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref -sf selection1.dat -sel -sf selection2.dat where the selections files are: selection1.dat: rdist = name CAL distance from name O22; name O22 and rdist <= 0.3; (for the first line I am following an example in the User guide) selection2.dat: name OH2 When attempting to run I get an error: Error in user input: Invalid command-line options In command-line option -sf Error in parsing selections from file 'selection1.dat' Invalid selection 'rdist = name CAL distance from name O22' syntax error In command-line option -sf Error in adding selections from file 'selection2.dat' Too few selections provided I guess the syntax of my selection instructions is wrong. Any help will be appreciated. Thanks, Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Wednesday, February 27, 2019 5:27 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi, One way to check that is to consult the online documentation... http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows options taking dynamic selections! Mark On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E wrote: > Hello all, > I would like to calculate the rdf between a set of oxygen atoms in a lipid > bilayer to water. But I would like to include in this calculation only a > subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I > wonder if such a dynamic selection is possible combined with the rdf tool. > Thanks > Alfredo Cardenas > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] can dynamic selection be used with gmx rdf?
Hi Mark, Thanks for your reply. I have tried the following run: gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref -sf selection1.dat -sel -sf selection2.dat where the selections files are: selection1.dat: rdist = name CAL distance from name O22; name O22 and rdist <= 0.3; (for the first line I am following an example in the User guide) selection2.dat: name OH2 When attempting to run I get an error: Error in user input: Invalid command-line options In command-line option -sf Error in parsing selections from file 'selection1.dat' Invalid selection 'rdist = name CAL distance from name O22' syntax error In command-line option -sf Error in adding selections from file 'selection2.dat' Too few selections provided I guess the syntax of my selection instructions is wrong. Any help will be appreciated. Thanks, Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Wednesday, February 27, 2019 5:27 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi, One way to check that is to consult the online documentation... http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows options taking dynamic selections! Mark On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E wrote: > Hello all, > I would like to calculate the rdf between a set of oxygen atoms in a lipid > bilayer to water. But I would like to include in this calculation only a > subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I > wonder if such a dynamic selection is possible combined with the rdf tool. > Thanks > Alfredo Cardenas > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] can dynamic selection be used with gmx rdf?
Hi, One way to check that is to consult the online documentation... http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows options taking dynamic selections! Mark On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E wrote: > Hello all, > I would like to calculate the rdf between a set of oxygen atoms in a lipid > bilayer to water. But I would like to include in this calculation only a > subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I > wonder if such a dynamic selection is possible combined with the rdf tool. > Thanks > Alfredo Cardenas > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] can dynamic selection be used with gmx rdf?
Hello all, I would like to calculate the rdf between a set of oxygen atoms in a lipid bilayer to water. But I would like to include in this calculation only a subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I wonder if such a dynamic selection is possible combined with the rdf tool. Thanks Alfredo Cardenas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.