Re: [gmx-users] g_dist equivalent in Version 5.*
Hi, I did not know that you can explicitly specify Center of Masses using `-select` option. I was giving to input my whole selections (after command line prompt), and it was calculating something else, and I'm not sure what ) On Sat, Jan 26, 2019 at 9:27 PM laura O. wrote: > Hi, > > gmx distance can compute distances of mass center's, right? > > Im was the same problem and i use: gmx distance -n index.ndx -select 'com > of group "A" plus com of group "B"'. > > A and B can be numbers or words. > > What did you mean "but it calculates pairwise distances in one selection" ? > How is this selection made? You can tell me something else about this > because I have this question too. > > > Thanks > > Em sáb, 26 de jan de 2019 às 05:39, Max Adamyan > escreveu: > > > Thanks a lot. This does indeed help) > > > > Sincerely > >Max. > > > > > On Jan 25, 2019, at 22:09, Mark Abraham > > wrote: > > > > > > Hi, > > > > > > Does > > > > > > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions > > > help? > > > > > > Mark > > > > > >> On Fri., 25 Jan. 2019, 10:29 Max Adamyan, > > wrote: > > >> > > >> Hi. I know you can compute distances of mass center's of two atom > groups > > >> using `g_dist` command. But I cannot find command that does the same > in > > >> Gromacs version 5.* > > >> I know `gmx distance`, but it calculates pairwise distances in one > > >> selection. > > >> And `gmx pairdist` which calculates only min or max distances. > > >> None of this is what I want, I cannot find any other distance related > > >> commands. > > >> Is there any? > > >> Thanks. > > >> -- > > >> Sincerely, > > >>Max Adamyan > > >> -- > > >> 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. -- Sincerely, Max Adamyan -- 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] g_dist equivalent in Version 5.*
Hi, gmx distance can compute distances of mass center's, right? Im was the same problem and i use: gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"'. A and B can be numbers or words. What did you mean "but it calculates pairwise distances in one selection" ? How is this selection made? You can tell me something else about this because I have this question too. Thanks Em sáb, 26 de jan de 2019 às 05:39, Max Adamyan escreveu: > Thanks a lot. This does indeed help) > > Sincerely >Max. > > > On Jan 25, 2019, at 22:09, Mark Abraham > wrote: > > > > Hi, > > > > Does > > > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions > > help? > > > > Mark > > > >> On Fri., 25 Jan. 2019, 10:29 Max Adamyan, > wrote: > >> > >> Hi. I know you can compute distances of mass center's of two atom groups > >> using `g_dist` command. But I cannot find command that does the same in > >> Gromacs version 5.* > >> I know `gmx distance`, but it calculates pairwise distances in one > >> selection. > >> And `gmx pairdist` which calculates only min or max distances. > >> None of this is what I want, I cannot find any other distance related > >> commands. > >> Is there any? > >> Thanks. > >> -- > >> Sincerely, > >>Max Adamyan > >> -- > >> 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] g_dist equivalent in Version 5.*
Thanks a lot. This does indeed help) Sincerely Max. > On Jan 25, 2019, at 22:09, Mark Abraham wrote: > > Hi, > > Does > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions > help? > > Mark > >> On Fri., 25 Jan. 2019, 10:29 Max Adamyan, wrote: >> >> Hi. I know you can compute distances of mass center's of two atom groups >> using `g_dist` command. But I cannot find command that does the same in >> Gromacs version 5.* >> I know `gmx distance`, but it calculates pairwise distances in one >> selection. >> And `gmx pairdist` which calculates only min or max distances. >> None of this is what I want, I cannot find any other distance related >> commands. >> Is there any? >> Thanks. >> -- >> Sincerely, >>Max Adamyan >> -- >> 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] g_dist equivalent in Version 5.*
Hi, Does http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#command-changes-between-versions help? Mark On Fri., 25 Jan. 2019, 10:29 Max Adamyan, wrote: > Hi. I know you can compute distances of mass center's of two atom groups > using `g_dist` command. But I cannot find command that does the same in > Gromacs version 5.* > I know `gmx distance`, but it calculates pairwise distances in one > selection. > And `gmx pairdist` which calculates only min or max distances. > None of this is what I want, I cannot find any other distance related > commands. > Is there any? > Thanks. > -- > Sincerely, > Max Adamyan > -- > 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] g_dist tools
Hi, We can't tell what you want to do, so perhaps you should read the help for gmx distance and choose accordingly. Mark On Thu, Jun 4, 2015 at 9:13 PM Poncho Arvayo Zatarain poncho_8...@hotmail.com wrote: Hello, i want to run this command: echo 3 4| g_dist -f dppc128_1-nj-ct-nobox.xtc - s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 2 in Gromacs 5.0.4 but when i run it, the following appears: This tool has been removed. Please see tool changes for 5.0. And when i see th tools appears: g_dist: This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:gmx distance -n index.ndx -select 'com of group A plus com of group B' -oxyz -oall The -intra switch is replaced with -nopbc. If you used -dist D, you can do the same calculation with gmx select: gmx select -n index.ndx -select 'group B and within D of com of group A' -on/-oi/-os/-olt You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt) Shoukd i use -dist or -intra option? -- 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] g_dist
On 3/19/15 12:28 AM, RINU KHATTRI wrote: hello everyone i am unable to understand the result of gmx check .it gives frames and time values .g_dist is worked in all protein related residues but i want to calculate the distance between some residues of protein and ligand for ligand i got same problem like mismatch. The reason I had you use gmx check was to figure out how many atoms you saved in the trajectory. If it's fewer than the atom numbers specified in the index file, you have identified your problem. From your description, it sounds like you only saved protein coordinates during the run or in some trjconv post-processing task. You can't analyze something that's not there. -Justin kindly help On Mon, Mar 16, 2015 at 5:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/16/15 6:43 AM, RINU KHATTRI wrote: hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help So what does gmxcheck tell you about the contents of the .tpr and the .xtc? Likely you have a mismatch in what you saved to the trajectory either in the run or when using trjconv at some point. -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. -- == 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] g_dist
hello everyone i am unable to understand the result of gmx check .it gives frames and time values .g_dist is worked in all protein related residues but i want to calculate the distance between some residues of protein and ligand for ligand i got same problem like mismatch. kindly help On Mon, Mar 16, 2015 at 5:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/16/15 6:43 AM, RINU KHATTRI wrote: hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help So what does gmxcheck tell you about the contents of the .tpr and the .xtc? Likely you have a mismatch in what you saved to the trajectory either in the run or when using trjconv at some point. -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. -- 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] g_dist
On 3/16/15 6:43 AM, RINU KHATTRI wrote: hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help So what does gmxcheck tell you about the contents of the .tpr and the .xtc? Likely you have a mismatch in what you saved to the trajectory either in the run or when using trjconv at some point. -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] g_dist as an alternative for g _saltbr
On 10/17/14 2:13 PM, Diogo Martins de Sá wrote: Dear Justin, thanks for your reply. To start with, here are the links where you mentioned looping calculations (http://article.gmane.org/gmane.science.biology.gromacs.user/59569/match=g_saltbr+looping+calculations) and track persistence of interactions (http://www.researchgate.net/post/Can_anyone_help_with_salt_bridges_with_gromacs) Since g_saltbr is dumb in its main function (and should actually be called something like g_electrostaticInteractions), I've decided to tackle this question in the following manner: 1. I must use gromacs in way where I find all the SBs in my system, and just those. 2. I must use gromacs to observe the distance of these SBs as a function of time. This is how I intend to do it. 1. Acording to Kumar Nussinov 2002 (Close-Range Electrostatic Interactions in Proteins), salt bridges must have at least a pair of sidechain functional-group nitrogen and oxygen atoms within 4 ä distance. So I will use g_select to create groups of ASP's GLU's sidechain Oxigen and respective hydrogens and HIS's, Lys's Arg's sidechain Nitrogen atoms and respective hydrogens. Why include the hydrogens? Because I'll need them to use g_hbond. Why use g_hbond? Because of the matrix. Why is the matrix so important? Because of your (Justin's) script that shows the percentage of time that a given hydrogen bond existed during the trajectory: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html. So I will run g_hbond with -r 0.49 (0.35 from hydrogen bond + 0.14 which is the furthest distance a covalently bonded hydrogen can be from nytrogen, this distance is 0.12 for oxigen. Hydrogen bonds pull the covalently bonded H away from atoms and this is directly proportional to the strengh of the bond). After this process, I will have all the salt bridges and the percentage of their appearence through the trajectory (thanks to your script). So I now I know which ones I should take a closer look. 2. To measure distance as function of time, I can use either g_bond (with -d) or g_dist. If I get few SBs after step 1, I will use g_dist, because then I will make individual groups. If I get more than a few SBs, g_bond can organize each one and I have to make only two groups. What do you (and any other user reading) think about this strategy? I do have one problem, I never used g_select and I'm having some difficuly understanding the syntax. Does any one know how I should call g_select so I create index groups like I mentioned in step 1?? Probably something that is even easier is to use trjconv to strip the groups of interest using a single index group (i.e. functional groups of interest), then use tpbconv (gmx convert-tpr in 5.0) to make a matching .tpr, then just use g_saltbr -t as needed. Saves a lot of work, and you're only ever looking at possible groups of interest. That circumvents the problem that g_saltbr doesn't accept an index group. trjconv and tpbconv do :) -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] g_dist as an alternative for g _saltbr
That can certainly work for me! Especially because I know my groups functional groups. I guess if one was still in doubt what to focus on, then my idea could still be useful (with a bit more of work). Now, just so I get things right: 1. I got to make ONE group in my .ndx that contains all my functional groups, and use trjconv to create a trajectory containing only those groups. 2. Same goes for .tpr 3. When I run g_saltbr I should use -sep, correct? or else I'm going to have problems viewing the distanceXtime graphics of all SBs using xmgrace. 4. Is the -t option measured in nm? Making the default 1um (micrometer)? If so, then I should change it from 1000 to 0.4? thanks again, Diogo Original Message Date: Fri, 17 Oct 2014 15:56:30 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_dist as an alternative for g _saltbr Message-ID: 5441746e.20...@vt.edu Content-Type: text/plain; charset=utf-8; format=flowed On 10/17/14 2:13 PM, Diogo Martins de S? wrote: Dear Justin, thanks for your reply. To start with, here are the links where you mentioned looping calculations (http://article.gmane.org/gmane.science.biology.gromacs.user/59569/match=g_saltbr+looping+calculations) and track persistence of interactions (http://www.researchgate.net/post/Can_anyone_help_with_salt_bridges_with_gromacs) Since g_saltbr is dumb in its main function (and should actually be called something like g_electrostaticInteractions), I've decided to tackle this question in the following manner: 1. I must use gromacs in way where I find all the SBs in my system, and just those. 2. I must use gromacs to observe the distance of these SBs as a function of time. This is how I intend to do it. 1. Acording to Kumar Nussinov 2002 (Close-Range Electrostatic Interactions in Proteins), salt bridges must have at least a pair of sidechain functional-group nitrogen and oxygen atoms within 4 ? distance. So I will use g_select to create groups of ASP's GLU's sidechain Oxigen and respective hydrogens and HIS's, Lys's Arg's sidechain Nitrogen atoms and respective hydrogens. Why include the hydrogens? Because I'll need them to use g_hbond. Why use g_hbond? Because of the matrix. Why is the matrix so important? Because of your (Justin's) script that shows the percentage of time that a given hydrogen bond existed during the trajectory: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html. So I will run g_hbond with -r 0.49 (0.35 from hydrogen bond + 0.14 which is the furthest distance a covalently bonded hydrogen can be from nytrogen, this distance is 0.12 for oxigen. Hydrogen bonds pull the covalently bonded H away from atoms and this is directly proportional to the strengh of the bond). After this process, I will have all the salt bridges and the percentage of their appearence through the trajectory (thanks to your script). So I now I know which ones I should take a closer look. 2. To measure distance as function of time, I can use either g_bond (with -d) or g_dist. If I get few SBs after step 1, I will use g_dist, because then I will make individual groups. If I get more than a few SBs, g_bond can organize each one and I have to make only two groups. What do you (and any other user reading) think about this strategy? I do have one problem, I never used g_select and I'm having some difficuly understanding the syntax. Does any one know how I should call g_select so I create index groups like I mentioned in step 1?? Probably something that is even easier is to use trjconv to strip the groups of interest using a single index group (i.e. functional groups of interest), then use tpbconv (gmx convert-tpr in 5.0) to make a matching .tpr, then just use g_saltbr -t as needed. Saves a lot of work, and you're only ever looking at possible groups of interest. That circumvents the problem that g_saltbr doesn't accept an index group. trjconv and tpbconv do :) -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] g_dist as an alternative for g _saltbr
On 10/17/14 4:49 PM, Diogo Martins de Sá wrote: That can certainly work for me! Especially because I know my groups functional groups. I guess if one was still in doubt what to focus on, then my idea could still be useful (with a bit more of work). Now, just so I get things right: 1. I got to make ONE group in my .ndx that contains all my functional groups, and use trjconv to create a trajectory containing only those groups. 2. Same goes for .tpr Correct. 3. When I run g_saltbr I should use -sep, correct? or else I'm going to have problems viewing the distanceXtime graphics of all SBs using xmgrace. Probably a good idea to write everything separately. 4. Is the -t option measured in nm? Making the default 1um (micrometer)? If so, then I should change it from 1000 to 0.4? Yes, Gromacs always uses nm as the default distance unit. The default behavior basically says consider everything possible. -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] g_dist as an alternative for g_saltbr
On 10/15/14 2:19 PM, Diogo Martins de Sá wrote: Fellow users, I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where you already know which are the SBs present in the system. If one has this information, he could easily create groups of individual residues (which would actually contain just the ionazable atoms and their hydrogens, depricating the carbons and other atoms) and observe how the salt bridges behave. My question is concerning the situation where you still don't know which are the salt bridges in the system and, after that, which are the ones you should take a closer look (I think the obvious approach would be to search literature, but that is not always successful). Justin Lemkul has mentioned, in two diferent discussions, using g_dist to track persistence of interactions and looping calculations to address the situation I've just mentioned. Could someone elaborate on those? I am confused as to what they actually mean and how to proceed (especially in the case of looping calculations). Likely I was referring to looping over calls to g_dist (in the future, please link to any previous discussions - it's hard for me to keep track of all of the thousands of messages I've sent :) One can certainly use g_saltbr to look at positive-negative interactions en masse, but it's a fairly dumb program, in that it considers a huge amount of groups that don't matter. You can weed through all of that to find things that might be of interest. -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] g_dist
On 12/29/13, 8:17 AM, Andrew Bostick wrote: Dear gromacs users I know g_dist tool calculates the distance between the centers of mass of two groups of atoms as a function of time. How to obtain average distances of the selected atoms form the bilayer midplane. In this case, one group is selected atoms, but another group? If you are interested in the bilayer midplane, then selecting the entire bilayer as the other group is appropriate. Is g_dist appropriate for this case? How? If you are not interested in the exact COM distance, but instead the distance between the group and the midplane, then looking only at the z-component of the COM distance seems to make sense, given that you would be uninterested in the x- and y-components of the distance, if the membrane is in the x-y plane. -Justin -- == 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.
