Re: [gmx-users] selection around circle
On 12/18/13 3:33 AM, jkrie...@mrc-lmb.cam.ac.uk wrote: Does it make sense to install gromacs 5.0 beta for analysing a simulation from 4.6.x? The 4.6.x series can't handle the g_select output (different index groups for each frame), so it's not really possible to (easily) make use of it. One could, of course, write a script to dump out every frame separately, run the analysis on that frame using the corresponding index group, then assemble the output into something useful. But if 5.0 beta does all of that seamlessly, why wouldn't you take advantage of that? -Justin On 18 Dec 2013, at 05:17, Venkat Reddy wrote: Hi, I have had used 5.0 beta version and as far as I know, "gmx gangle" supports the output from g_select. On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul wrote: On 12/17/13 7:43 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: Thanks Justin, I have tried this and I can a new index file that has an item for each frame with atoms that match the selection. How do I create a single index item and combine it into the main index file for use with other tools such as g_hbond? The output of g_select is not fully compatible with any Gromacs tool, at least in any pre-5.0 version. Given that I have had not had time yet to fully investigate the current beta, hopefully someone else can say whether or not the g_select output is now fully supported by other tools. -Justin Best wishes James On 18 Dec 2013, at 00:14, Justin Lemkul wrote: On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. The examples at the end of g_select -select 'help all' pretty well cover most of these situations. What have you tried? What has it given you? Something like: same residue as resname SOL and within 0.5 of residue X provided that residue X is defined within an .ndx file provided on the command, line should work. Disclaimer: this is just off the cuff, but probably pretty close. -Justin Dear Gmx Users, I have my carbon nanotube (lenght z axis) with proteins attached to it. I wish to collect RDF of given type of amino acids away from the surface in two dimensions (xy). Z axis does not interest me. That would make a circle then. My question: how to make a specific index group of this circle? Any ideas appreciated. Steven -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20
Re: [gmx-users] selection around circle
Does it make sense to install gromacs 5.0 beta for analysing a simulation from 4.6.x? On 18 Dec 2013, at 05:17, Venkat Reddy wrote: > Hi, > I have had used 5.0 beta version and as far as I know, "gmx gangle" > supports the output from g_select. > > > On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul wrote: > >> >> >> On 12/17/13 7:43 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: >> >>> Thanks Justin, >>> >>> I have tried this and I can a new index file that has an item for each >>> frame with atoms that match the selection. How do I create a single index >>> item and combine it into the main index file for use with other tools such >>> as g_hbond? >> The output of g_select is not fully compatible with any Gromacs tool, at >> least in any pre-5.0 version. Given that I have had not had time yet to >> fully investigate the current beta, hopefully someone else can say whether >> or not the g_select output is now fully supported by other tools. >> >> -Justin >> >> >> Best wishes >>> James >>> >>> On 18 Dec 2013, at 00:14, Justin Lemkul wrote: >>> >>> On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: > I think g_select does something like this. I am trying to do something > similar: make a selection of water within 5A or so of a residue in my > protein. Also need help please. The examples at the end of g_select -select 'help all' pretty well cover most of these situations. What have you tried? What has it given you? Something like: same residue as resname SOL and within 0.5 of residue X provided that residue X is defined within an .ndx file provided on the command, line should work. Disclaimer: this is just off the cuff, but probably pretty close. -Justin Dear Gmx Users, >> >> I have my carbon nanotube (lenght z axis) with proteins attached to >> it. I >> wish to collect RDF of given type of amino acids away from the surface >> in >> two dimensions (xy). Z axis does not interest me. That would make a >> circle >> then. My question: how to make a specific index group of this circle? >> Any >> ideas appreciated. >> >> Steven >> -- >> 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >> == >> -- >> 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. > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > 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/
Re: [gmx-users] selection around circle
Hi, I have had used 5.0 beta version and as far as I know, "gmx gangle" supports the output from g_select. On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul wrote: > > > On 12/17/13 7:43 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: > >> Thanks Justin, >> >> I have tried this and I can a new index file that has an item for each >> frame with atoms that match the selection. How do I create a single index >> item and combine it into the main index file for use with other tools such >> as g_hbond? >> >> > The output of g_select is not fully compatible with any Gromacs tool, at > least in any pre-5.0 version. Given that I have had not had time yet to > fully investigate the current beta, hopefully someone else can say whether > or not the g_select output is now fully supported by other tools. > > -Justin > > > Best wishes >> James >> >> On 18 Dec 2013, at 00:14, Justin Lemkul wrote: >> >> >>> >>> On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: >>> I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. >>> >>> The examples at the end of g_select -select 'help all' pretty well cover >>> most of these situations. What have you tried? What has it given you? >>> Something like: >>> >>> same residue as resname SOL and within 0.5 of residue X >>> >>> provided that residue X is defined within an .ndx file provided on the >>> command, line should work. Disclaimer: this is just off the cuff, but >>> probably pretty close. >>> >>> -Justin >>> >>> Dear Gmx Users, > > I have my carbon nanotube (lenght z axis) with proteins attached to > it. I > wish to collect RDF of given type of amino acids away from the surface > in > two dimensions (xy). Z axis does not interest me. That would make a > circle > then. My question: how to make a specific index group of this circle? > Any > ideas appreciated. > > Steven > -- > 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. > >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> == >>> -- >>> 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. >>> >> > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] selection around circle
On 12/17/13 7:43 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: Thanks Justin, I have tried this and I can a new index file that has an item for each frame with atoms that match the selection. How do I create a single index item and combine it into the main index file for use with other tools such as g_hbond? The output of g_select is not fully compatible with any Gromacs tool, at least in any pre-5.0 version. Given that I have had not had time yet to fully investigate the current beta, hopefully someone else can say whether or not the g_select output is now fully supported by other tools. -Justin Best wishes James On 18 Dec 2013, at 00:14, Justin Lemkul wrote: On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. The examples at the end of g_select -select 'help all' pretty well cover most of these situations. What have you tried? What has it given you? Something like: same residue as resname SOL and within 0.5 of residue X provided that residue X is defined within an .ndx file provided on the command, line should work. Disclaimer: this is just off the cuff, but probably pretty close. -Justin Dear Gmx Users, I have my carbon nanotube (lenght z axis) with proteins attached to it. I wish to collect RDF of given type of amino acids away from the surface in two dimensions (xy). Z axis does not interest me. That would make a circle then. My question: how to make a specific index group of this circle? Any ideas appreciated. Steven -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] selection around circle
Thanks Justin, I have tried this and I can a new index file that has an item for each frame with atoms that match the selection. How do I create a single index item and combine it into the main index file for use with other tools such as g_hbond? Best wishes James On 18 Dec 2013, at 00:14, Justin Lemkul wrote: > > > On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: >> I think g_select does something like this. I am trying to do something >> similar: make a selection of water within 5A or so of a residue in my >> protein. Also need help please. > > The examples at the end of g_select -select 'help all' pretty well cover most > of these situations. What have you tried? What has it given you? Something > like: > > same residue as resname SOL and within 0.5 of residue X > > provided that residue X is defined within an .ndx file provided on the > command, line should work. Disclaimer: this is just off the cuff, but > probably pretty close. > > -Justin > >>> Dear Gmx Users, >>> >>> I have my carbon nanotube (lenght z axis) with proteins attached to it. I >>> wish to collect RDF of given type of amino acids away from the surface in >>> two dimensions (xy). Z axis does not interest me. That would make a circle >>> then. My question: how to make a specific index group of this circle? Any >>> ideas appreciated. >>> >>> Steven >>> -- >>> 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. > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > 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] selection around circle
On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. The examples at the end of g_select -select 'help all' pretty well cover most of these situations. What have you tried? What has it given you? Something like: same residue as resname SOL and within 0.5 of residue X provided that residue X is defined within an .ndx file provided on the command, line should work. Disclaimer: this is just off the cuff, but probably pretty close. -Justin Dear Gmx Users, I have my carbon nanotube (lenght z axis) with proteins attached to it. I wish to collect RDF of given type of amino acids away from the surface in two dimensions (xy). Z axis does not interest me. That would make a circle then. My question: how to make a specific index group of this circle? Any ideas appreciated. Steven -- 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. -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] selection around circle
I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. > Dear Gmx Users, > > I have my carbon nanotube (lenght z axis) with proteins attached to it. I > wish to collect RDF of given type of amino acids away from the surface in > two dimensions (xy). Z axis does not interest me. That would make a circle > then. My question: how to make a specific index group of this circle? Any > ideas appreciated. > > Steven > -- > 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.
