[gmx-users] gmx select
Hi all, I'm trying to work out how many molecules of ligand and water I have within a certain distance. I used the gmx select command below: gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname LIG and within 0.5 of whole_res_com of resnr 1' -dt 100 However, this only outputs atomic positions. How can I get the number of "whole molecules"? If that makes sense? Or is there another command I can use? Akash -- 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] gmx select help
Hi all, I am running the gmx select command to create a file with all my ligand molecules that are within the cut-off distance specified from the COM of a protein residue as a function of time. Here is the command I am using: gmx select -f traj2.gro -s protein.tpr -dt 100 -on index.ndx -select 'resname LIG and within 0.5 of res_com of resnr 183' -resnr number The file currently outputs atom numbers for my ligand molecules. If I only wanted the resid of my ligands (as named in the trajectory file, e.g. resid 130 LIG) instead of the atom id to be written, how would I do this? Akash -- 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] gmx select
Hi all, I am running the gmx select command to obtain all my ligand molecules that are within a cut-off distance from the COM of a protein residue as a function of time. The output from the command below comes with just the atom positions of my ligand. gmx select -f protein_gly.gro -s protein.tpr -n mindist1.ndx -dt 100 -oi index.dat -select 'resname LIG and within 3 of res_com of resnr 183' -resnr index Is there a way to only output the residue number instead of the atom numbers? Akash -- 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] gmx select with coordinates
Hi Prof. Dan, Thank you very much for the e-mail. How do we define coordinates what we want in VMD Graphical Representation menu? Thank you. On Wed, Oct 10, 2018 at 6:53 AM Dan Gil wrote: > Hi Shan, > > Sorry it's been a while - I don't check this email too often. Did you > figure the problem out? > > I use the Graphical Representations menu of VMD, although I am sure there > is a way to do it in the console too. > > On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Prof. Dan, > > > > Thank you very much for the suggestion. However, when I gave the command; > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in > > VMD TkConsole, I didn't get any output. > > > > I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 > > and y. What could be the reason for this? Appreciate, if you can reply > me. > > > > Thank you. > > > > On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > > > > > Hi, > > > > > > I believe you are trying to select atoms/particles that are in an > > > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and > > > (90, 125)? > > > > > > Gmx select uses commands that are similar in syntax to a software > called > > > VMD. So I like to use VMD to figure out what I need to give to gmx > select > > > in order to get the selections I want. > > > > > > For example, I think for what you want, I would do: > > > > > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > [Press Enter] > > > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] > > > > > > If you want to include it in a script without manual user input: > > > > > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc > > -s > > > run05.tpr -b 39 -e 40 -on index.ndx > > > > > > VMD is great! It's also free software if you haven't tried using it > yet. > > > The only thing you gotta watch out for is that VMD uses Angstroms while > > GMX > > > uses nm. > > > > > > Dan > > > > > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < > > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > Dear Gromacs users, > > > > > > > > I want to make an index files with molecules in a particular area. I > > have > > > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] > > which > > > > define an area of the system. How can I do it with gmx_select? > > > > > > > > Can anyone help me? > > > > > > > > Thank you. > > > > > > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > > > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > > > > > > > > Dear Gromacs users, > > > > > > > > > > I want to make an index files with particular x and y coordinates. > > > There > > > > > is no restriction for z coordinates. How can I do it with > > gmx_select? I > > > > > already tried with the following command. However, it seems I don't > > get > > > > the > > > > > result I want. > > > > > > > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > > > > > > > Can anyone help me? > > > > > > > > > > Thank you. > > > > > > > > > > > > > > > > > -- > > > > Best Regards > > > > Shan Jayasinghe > > > > -- > > > > 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. > > > > > > > > > -- > > Best Regards > > Shan Jayasinghe > > -- > > 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. > -- Best Regards
Re: [gmx-users] gmx select with coordinates
Hi Shan, Sorry it's been a while - I don't check this email too often. Did you figure the problem out? I use the Graphical Representations menu of VMD, although I am sure there is a way to do it in the console too. On Thu, Sep 27, 2018 at 9:35 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Prof. Dan, > > Thank you very much for the suggestion. However, when I gave the command; > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in > VMD TkConsole, I didn't get any output. > > I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 > and y. What could be the reason for this? Appreciate, if you can reply me. > > Thank you. > > On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > > > Hi, > > > > I believe you are trying to select atoms/particles that are in an > > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and > > (90, 125)? > > > > Gmx select uses commands that are similar in syntax to a software called > > VMD. So I like to use VMD to figure out what I need to give to gmx select > > in order to get the selections I want. > > > > For example, I think for what you want, I would do: > > > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > [Press Enter] > > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] > > > > If you want to include it in a script without manual user input: > > > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc > -s > > run05.tpr -b 39 -e 40 -on index.ndx > > > > VMD is great! It's also free software if you haven't tried using it yet. > > The only thing you gotta watch out for is that VMD uses Angstroms while > GMX > > uses nm. > > > > Dan > > > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> wrote: > > > > > Dear Gromacs users, > > > > > > I want to make an index files with molecules in a particular area. I > have > > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] > which > > > define an area of the system. How can I do it with gmx_select? > > > > > > Can anyone help me? > > > > > > Thank you. > > > > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > > > > > Dear Gromacs users, > > > > > > > > I want to make an index files with particular x and y coordinates. > > There > > > > is no restriction for z coordinates. How can I do it with > gmx_select? I > > > > already tried with the following command. However, it seems I don't > get > > > the > > > > result I want. > > > > > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > > > > > Can anyone help me? > > > > > > > > Thank you. > > > > > > > > > > > > > -- > > > Best Regards > > > Shan Jayasinghe > > > -- > > > 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. > > > > > -- > Best Regards > Shan Jayasinghe > -- > 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] gmx select with coordinates
Dear Prof. Dan, Thank you very much for the suggestion. However, when I gave the command; gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx in VMD TkConsole, I didn't get any output. I didn't get the cursor in next line to type x > 45 and x < 90 and y > 90 and y. What could be the reason for this? Appreciate, if you can reply me. Thank you. On Fri, Sep 28, 2018 at 12:00 AM Dan Gil wrote: > Hi, > > I believe you are trying to select atoms/particles that are in an > infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and > (90, 125)? > > Gmx select uses commands that are similar in syntax to a software called > VMD. So I like to use VMD to figure out what I need to give to gmx select > in order to get the selections I want. > > For example, I think for what you want, I would do: > > gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > [Press Enter] > x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] > > If you want to include it in a script without manual user input: > > echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s > run05.tpr -b 39 -e 40 -on index.ndx > > VMD is great! It's also free software if you haven't tried using it yet. > The only thing you gotta watch out for is that VMD uses Angstroms while GMX > uses nm. > > Dan > > On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > Dear Gromacs users, > > > > I want to make an index files with molecules in a particular area. I have > > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which > > define an area of the system. How can I do it with gmx_select? > > > > Can anyone help me? > > > > Thank you. > > > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > > shanjayasinghe2...@gmail.com> wrote: > > > > > > > > Dear Gromacs users, > > > > > > I want to make an index files with particular x and y coordinates. > There > > > is no restriction for z coordinates. How can I do it with gmx_select? I > > > already tried with the following command. However, it seems I don't get > > the > > > result I want. > > > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > > > Can anyone help me? > > > > > > Thank you. > > > > > > > > > -- > > Best Regards > > Shan Jayasinghe > > -- > > 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. > -- Best Regards Shan Jayasinghe -- 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] gmx select with coordinates
Hi, I believe you are trying to select atoms/particles that are in an infinitely tall box with the vertices (45, 90), (45, 125), (90, 90) and (90, 125)? Gmx select uses commands that are similar in syntax to a software called VMD. So I like to use VMD to figure out what I need to give to gmx select in order to get the selections I want. For example, I think for what you want, I would do: gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx [Press Enter] x > 45 and x < 90 and y > 90 and y < 125 [Press Enter] If you want to include it in a script without manual user input: echo x > 45 and x < 90 and y > 90 and y < 125 | gmx select -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx VMD is great! It's also free software if you haven't tried using it yet. The only thing you gotta watch out for is that VMD uses Angstroms while GMX uses nm. Dan On Thu, Sep 27, 2018 at 7:51 AM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs users, > > I want to make an index files with molecules in a particular area. I have > four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which > define an area of the system. How can I do it with gmx_select? > > Can anyone help me? > > Thank you. > > On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < > shanjayasinghe2...@gmail.com> wrote: > > > > > Dear Gromacs users, > > > > I want to make an index files with particular x and y coordinates. There > > is no restriction for z coordinates. How can I do it with gmx_select? I > > already tried with the following command. However, it seems I don't get > the > > result I want. > > > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > > > Can anyone help me? > > > > Thank you. > > > > > -- > Best Regards > Shan Jayasinghe > -- > 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] gmx select with coordinates
Dear Gromacs users, I want to make an index files with molecules in a particular area. I have four x,y coordinates [(45, 90), (45, 125), (90, 90) and (90, 125)] which define an area of the system. How can I do it with gmx_select? Can anyone help me? Thank you. On Thu, Sep 27, 2018 at 4:14 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > > Dear Gromacs users, > > I want to make an index files with particular x and y coordinates. There > is no restriction for z coordinates. How can I do it with gmx_select? I > already tried with the following command. However, it seems I don't get the > result I want. > > gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f > run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx > > Can anyone help me? > > Thank you. > -- Best Regards Shan Jayasinghe -- 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] gmx select with coordinates
Dear Gromacs users, I want to make an index files with particular x and y coordinates. There is no restriction for z coordinates. How can I do it with gmx_select? I already tried with the following command. However, it seems I don't get the result I want. gmx select '[45, 90] and [45, 125] and [90, 90] and [90, 125]' -f run05.xtc -s run05.tpr -b 39 -e 40 -on index.ndx Can anyone help me? Thank you. -- 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] gmx select and gmx trjconv or gmx density
Thank you Dr. Abraham! I think I will write a script to do the analysis then. Best Regards, Dan On Mon, Apr 9, 2018 at 12:57 PM, Mark Abrahamwrote: > Hi, > > Unfortunately not all tools support dynamic selection groups yet, so the > only useful way to use that index file is by matching it with the correct > single frame from the trajectory, which you might get from e.g. gmx trjconv > split > > Mark > > On Fri, Apr 6, 2018, 21:37 Dan Gil wrote: > > > Hi, > > > > I am trying to select particles that are z < 20 and z > 10 as a function > of > > time. > > > > I think I used gmx select correctly and generated an index file with > group > > names like "(z_<_.8_f2882_t23056.000)" > > > > Now I am unsure how I use this index file for gmx trjconv or gmx density. > > Does anybody have some advice? > > > > Thanks in advance. > > > > Best Regards, > > > > Dan Gil > > PhD Student > > Case Western Reserve University > > Department of Chemical and Biomolecular Engineering > > -- > > 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] gmx select and gmx trjconv or gmx density
Hi, Unfortunately not all tools support dynamic selection groups yet, so the only useful way to use that index file is by matching it with the correct single frame from the trajectory, which you might get from e.g. gmx trjconv split Mark On Fri, Apr 6, 2018, 21:37 Dan Gilwrote: > Hi, > > I am trying to select particles that are z < 20 and z > 10 as a function of > time. > > I think I used gmx select correctly and generated an index file with group > names like "(z_<_.8_f2882_t23056.000)" > > Now I am unsure how I use this index file for gmx trjconv or gmx density. > Does anybody have some advice? > > Thanks in advance. > > Best Regards, > > Dan Gil > PhD Student > Case Western Reserve University > Department of Chemical and Biomolecular Engineering > -- > 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] gmx select and gmx trjconv or gmx density
Hi, I am trying to select particles that are z < 20 and z > 10 as a function of time. I think I used gmx select correctly and generated an index file with group names like "(z_<_.8_f2882_t23056.000)" Now I am unsure how I use this index file for gmx trjconv or gmx density. Does anybody have some advice? Thanks in advance. Best Regards, Dan Gil PhD Student Case Western Reserve University Department of Chemical and Biomolecular Engineering -- 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] gmx select querry
Hello All, I have a question regarding the usage of gmx select. I want to select water molecules in a particular subset in z-direction (example z > 5 and z < 10) for each frame of my trajectory and then carry out analysis using g_mindist on each frame of the trajectory (with selections) For example: system consists of peptide 1 and peptide2, membrane, water and ions. using g_mindist, I want to calculate the number of contacts peptide1 is making with water vs. peptide2 in z >5 and z < 10 over the whole trajectory. When I try to make selection using: The option pdbatoms selected only lists the selected atoms. The option pdbatoms all lists everything. The -on options gives me the index file of only selected atoms: gmx_mpi select -f 432000g1.gro -s ../../3run_npt_noposre.tpr -select '(resname TIP3 and name OH2) and z > -10 and z < 20' -oi -pdbatoms selected -on insel.ndx I am a little confused how to incoporate the slections in odere to carry out the analysis I am interested in. Kindly suggest. Thanks for your time in advance. Regards, sn -- 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] gmx select
On 7/13/17 10:01 AM, Pandya, Akash wrote: So I tried with both opening and closing. It seems to select all the molecules in my box which is not what I want. I only want certain glycine molecules that are closest to the protein. May you please suggest another way is which I could achieve this. The command I used is below: gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb "resname Glycine" surely will return nothing. You need to use valid residue names as found in the .gro file. The format of .gro permits residue names up to 5 characters, so clearly "Glycine" is never going to match anything. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] gmx select
So I tried with both opening and closing. It seems to select all the molecules in my box which is not what I want. I only want certain glycine molecules that are closest to the protein. May you please suggest another way is which I could achieve this. The command I used is below: gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 13 July 2017 14:01 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select On 7/13/17 3:38 AM, Pandya, Akash wrote: > gmx select -f output.gro -select "Close to protein" resname Glyci and within > 0.5 of group "Protein"' > I suspect Mark is right, this is an invalid command, because you have a closing ' without an opening ' in your -select argument. This should fail with a generic error message that the selection can't be parsed. I am also curious about "resname Glyci" because if that's the case, then you must have hacked some force field files, because everyone calls glycine "GLY" per standard nomenclature. -Justin > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Mark Abraham > Sent: 13 July 2017 00:04 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > Can you please copy, paste and post your actual commands. I don't think your > use of quote marks would have led to a valid shell command. The whole > selection text will need to be inside some quotes. > > Mark > > On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > >> I have used the same name in my coordinate file. For Glycine it is >> spelt as Glyci, so the word has been cut off. I know this is correct >> because I use the same name in VMD. >> >> -Original Message- >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark >> Abraham >> Sent: 12 July 2017 22:42 >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] gmx select >> >> Hi, >> >> What are the residue names in your coordinate file? Glyci probably >> doesn't fit >> >> Mark >> >> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash >> <akash.pandya...@ucl.ac.uk> >> wrote: >> >>> Hi all, >>> >>> >>> I am trying to select all the glycine molecules with 0.5nm of my protein. >>> I tried both of these commands I got from the gromacs website: >>> >>> gmx select -f output.gro -select "Close to protein" resname Glyci >>> and within 0.5 of group "Protein"' -ofpdb >>> >>> gmx select -f output.xtc -s output.tpr (my converted input file) >>> -select "Close to protein" resname Glyci and within 0.5 of group >>> "Protein"' -ofpdb >>> >>> >>> Nothing comes up when I enter them. Please could someone help me >>> with >> this? >>> >>> >>> Akash >>> -- >>> 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
Re: [gmx-users] gmx select
On 7/13/17 3:38 AM, Pandya, Akash wrote: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' I suspect Mark is right, this is an invalid command, because you have a closing ' without an opening ' in your -select argument. This should fail with a generic error message that the selection can't be parsed. I am also curious about "resname Glyci" because if that's the case, then you must have hacked some force field files, because everyone calls glycine "GLY" per standard nomenclature. -Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 13 July 2017 00:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: I have used the same name in my coordinate file. For Glycine it is spelt as Glyci, so the word has been cut off. I know this is correct because I use the same name in VMD. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 12 July 2017 22:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: Hi all, I am trying to select all the glycine molecules with 0.5nm of my protein. I tried both of these commands I got from the gromacs website: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb Nothing comes up when I enter them. Please could someone help me with this? Akash -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] gmx select
gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 13 July 2017 00:04 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > I have used the same name in my coordinate file. For Glycine it is > spelt as Glyci, so the word has been cut off. I know this is correct > because I use the same name in VMD. > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 12 July 2017 22:42 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > What are the residue names in your coordinate file? Glyci probably > doesn't fit > > Mark > > On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash > <akash.pandya...@ucl.ac.uk> > wrote: > > > Hi all, > > > > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > > I tried both of these commands I got from the gromacs website: > > > > gmx select -f output.gro -select "Close to protein" resname Glyci > > and within 0.5 of group "Protein"' -ofpdb > > > > gmx select -f output.xtc -s output.tpr (my converted input file) > > -select "Close to protein" resname Glyci and within 0.5 of group > > "Protein"' -ofpdb > > > > > > Nothing comes up when I enter them. Please could someone help me > > with > this? > > > > > > Akash > > -- > > 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. -- 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] gmx select
Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > I have used the same name in my coordinate file. For Glycine it is spelt > as Glyci, so the word has been cut off. I know this is correct because I > use the same name in VMD. > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 12 July 2017 22:42 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx select > > Hi, > > What are the residue names in your coordinate file? Glyci probably doesn't > fit > > Mark > > On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> > wrote: > > > Hi all, > > > > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > > I tried both of these commands I got from the gromacs website: > > > > gmx select -f output.gro -select "Close to protein" resname Glyci and > > within 0.5 of group "Protein"' -ofpdb > > > > gmx select -f output.xtc -s output.tpr (my converted input file) > > -select "Close to protein" resname Glyci and within 0.5 of group > > "Protein"' -ofpdb > > > > > > Nothing comes up when I enter them. Please could someone help me with > this? > > > > > > Akash > > -- > > 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] gmx select
I have used the same name in my coordinate file. For Glycine it is spelt as Glyci, so the word has been cut off. I know this is correct because I use the same name in VMD. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 12 July 2017 22:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx select Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya...@ucl.ac.uk> wrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I got from the gromacs website: > > gmx select -f output.gro -select "Close to protein" resname Glyci and > within 0.5 of group "Protein"' -ofpdb > > gmx select -f output.xtc -s output.tpr (my converted input file) > -select "Close to protein" resname Glyci and within 0.5 of group > "Protein"' -ofpdb > > > Nothing comes up when I enter them. Please could someone help me with this? > > > Akash > -- > 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] gmx select
Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akashwrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I got from the gromacs website: > > gmx select -f output.gro -select "Close to protein" resname Glyci and > within 0.5 of group "Protein"' -ofpdb > > gmx select -f output.xtc -s output.tpr (my converted input file) -select > "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb > > > Nothing comes up when I enter them. Please could someone help me with this? > > > Akash > -- > 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] gmx select
Hi all, I am trying to select all the glycine molecules with 0.5nm of my protein. I tried both of these commands I got from the gromacs website: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb gmx select -f output.xtc -s output.tpr (my converted input file) -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb Nothing comes up when I enter them. Please could someone help me with this? Akash -- 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] gmx select
Dear all, I am a little bit lost with the use of select. I am looking at a protein in a water:glycerol mixture. I would like to count how many glycerol molecules there are within 3Angstrom of the protein. I first used the following command to count the central atom (named C2): gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none -select "name C2 and within 0.3 of group Protein" This gives me on average over the trajectory 3.3. Then I wanted to count for the center of mass of glycerols, which shouldn't be too far from the central atom: gmx select -s File.gro -f File.xtc -n Index.ndx -os Gly-0.3.xvg -xvg none -select "res_com of resname GOL and within 0.3 of group Protein" There I found 58.4. I got the same result with whole_res_com than with res_com, and with Gromacs 5.1.1, 5.1.2 and 2016. I am surprised by the difference. I suspect that the second command counts all the atoms. Can someone please tell me if the last command is correct, and if not tell me what would be the correct use of select to count the number of center of mass of the glycerol molecules that have their center of mass within 0.3nm of the protein. Thank you Nicolas PS: I posted this question on the list a week ago but not sure it went through, sorry for the double posting -- 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.