Re: [gmx-users] hbond calculation in peptide-membrane simulation
What have you tried? What results did you get? Highly recommend you try things out, experiment, see what happens. That is faster and you learn more than having to wait for someone on an emailing list to reply. Search engine is very helpful too. http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-hbond.html - "You need to specify two groups for analysis, which must be either identical or non-overlapping. All hydrogen bonds between the two groups are analyzed." To make index groups - http://manual.gromacs.org/documentation/2016.4/onlinehelp/gmx-make_ndx.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 15 Oct 2018 at 18:15, manindersingh rajawat wrote: > > Dear gromacs users, > I performed 200ns MD simulations (gromacs 5.0.7) of peptide and mixed lipid > bilayer (POPS:POPC). Initially placed 6 copies of the peptide parallely > over the surface of the lipid bilayer (128 lipids). I want to calculate > hydrogen bond occupancy using hbond tool between peptide and lipids over > the simulation time. How to make index file for it. What atoms I should put > in index file. > Please advise with appropriate commands. > Thanks and regards, > Maninder > > > -- > Maninder Singh > Research Fellow, > LSN-104, Computational Biology and Bioinformatics Unit, > Molecular and Structural Biology Division, > CSIR-Central Drug Research Institute, > Sector-10, Janakipuram Extension, > Sitapur road, > Lucknow > India-226031 > M: +919129206276 > Email: rajawat.manindersi...@gmail.com > -- > 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] Hbond occupancy
>mmousivand93 > >Dear Dr.Dallas warren > >I am going to analysis H-bond and Hbond occupancy using readHBmap,I downloaded >and extracted readHBmap.tar.gz but after typing: ./readHBmap.py -hbm hbmap.xpm >-hbn hbond.ndx -f md6.gro -o occupancy.xvg -op pairs.dat ,the message "No >hydrogen bonds found above the threshold of 10.0 %%" will appear. The >pairs.dat and occupancy.xvg files are empty. When I opened the occupancy.xvg >by ConTexT ,the following results could be seen:" > >Results for readHBmap.py (Author: Ricardo O. S Soares) >--> Found 9 valid hydrogen bond pairs with occupancy of more than 10.0% >--> The hydrogen bond map (hbond.xpm) has 5001 frames > >Pair ID | donor-acceptor | Atom Number | Occupancy (%) | Pair ID > > I would appreciate any suggestions. > >Best regards Never used that script, so can't help you there. However, before using the script, does the hbmap.xpm file contain valid data that you would expect the script to be able to process? i.e. is the input into the script valid? If so, then might be an issue with the script, so contact that person that wrote it. They have provided their email address. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 8 Oct 2018 at 09:57, Dallas Warren wrote: > > What have you already tried? What results did you get? > > > First point of call should be http://manual.gromacs.org/documentation/ > > In particular > http://manual.gromacs.org/documentation/current/user-guide/cmdline.html > > There you can read through all the scripts that come with the software, how > to use them, and what data you can extract. > > Web searches, particularly of the emailing list, will provide lots of > information too. If after that, still have questions, then post to the > emailing list with what you want to do, what you have tried, and what you are > having problems with. > > On Sat, 6 Oct. 2018, 10:12 pm mmousivand93, wrote: >> >> Dear users >> >> I have run molecular dynamic for DNA-ligand complex and I am going to >> analysis H-bond and Hbond occupancy using GROMACS, I would appreciate >> any suggestions. >> >> Best regard >> -- >> 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] Hbond occupancy
What have you already tried? What results did you get? First point of call should be http://manual.gromacs.org/documentation/ In particular http://manual.gromacs.org/documentation/current/user-guide/cmdline.html There you can read through all the scripts that come with the software, how to use them, and what data you can extract. Web searches, particularly of the emailing list, will provide lots of information too. If after that, still have questions, then post to the emailing list with what you want to do, what you have tried, and what you are having problems with. On Sat, 6 Oct. 2018, 10:12 pm mmousivand93, wrote: > Dear users > > I have run molecular dynamic for DNA-ligand complex and I am going to > analysis H-bond and Hbond occupancy using GROMACS, I would appreciate > any suggestions. > > Best regard > -- > 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] Hbond residence time
On 4/24/17 9:45 PM, Marcelo Depólo wrote: Hi all! I have been looking into the autocorrelation function outputs of 'gmx hbond' in order to calculate the residence time for my water hbond to a specific heteroatom. It turns out that I couldn't find any detailed explanation about each 'type' outputted. In my case: Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2 Forward 3.384 0.296 1.506 0.0290557 Backward -0.183 -5.477-666.000 One-way 8.291 0.121 -0.716 Integral 0.802 1.247 5.075 Relaxation 0.767 1.303 5.185 Does anyone have a suggestion of what each of these types mean? All of that should be explained in the reference that gmx hbond printed to the terminal. -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] HBond for F and S (Justin Lemkul)
Thanks, Justin! It worked just fine. I guess using a flag to include different atomtypes into the analyses would be a nice feature for next GROMACS versions. Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center of Biotechnology - UFRGS Phone: + 55 51 3308-7770 -- 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] HBond for F and S
On 4/24/17 3:15 PM, Marcelo Depólo wrote: Hi, Can gmx hbond also calculates hbonds between non-canonical atoms like S or F as well? If so, how can I do it? Without changing the code, the only way to do it is to rename the atoms in the topology as some type of oxygen, create a new .tpr file, and use that .tpr file for the hydrogen bond analysis. -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] hbond error
On 2/16/17 9:17 AM, Mark Abraham wrote: Hi, Great. To check that I understand you, do you think it should it read "Ordering is the reverse of that in -hbn index file?" While this has been a point of confusion in the past, I think we have to be careful with the wording here. The ordering of -hbn and -hbm *is* actually the same (the first element in -hbn is in fact the first matrix element in -hbm), but the user has to understand how to interpret the contents of an .xpm file. Its contents are printed as one sees it visually, so the first line of data is the top line of the matrix, but that's not the first element of the matrix. So if we're going to clarify the language, we should probably have a rather more verbose explanation of how to map the entries, in terms of the .xpm content itself. -Justin Mark On Thu, Feb 16, 2017 at 2:32 PM wrote: Hi, I just realized that the hbond tool works fine, but produces output in reverse order. The "bug" is in the manual that states: * -hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file. Chiara Il 16/02/17 13:41, *Mark Abraham * ha scritto: Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: Dear Gmx users, using GROMACS version 2016.1, I found the following error in the output of the gmx hbond routine: when computed from different groups, where one is a subset of the other one, hbonds from the same acceptor/donor pair do not match. I known that this error has been already widely discussed in previous gromacs versions. Is there any solution? Thanks Chiara -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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. -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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] hbond error
Hi, Great. To check that I understand you, do you think it should it read "Ordering is the reverse of that in -hbn index file?" Mark On Thu, Feb 16, 2017 at 2:32 PM wrote: > Hi, > > I just realized that the hbond tool works fine, but produces output in > reverse order. The "bug" is in the manual that states: > > * -hbm: existence matrix for all hydrogen bonds over all frames, this > also > contains information on solvent insertion into hydrogen bonds. > Ordering is > identical to that in -hbn index file. > > Chiara > > Il 16/02/17 13:41, *Mark Abraham * ha scritto: > > Hi, > > > > I'm not sure whether I properly understand your description of the > > behaviour. But if you think you have a case where the tool doesn't do > what > > its documentation says, please open an issue at > > https://redmine.gromacs.org > > and attach a tarball of files that will help us diagnose and fix it :-) > > > > Mark > > > > On Thu, 16 Feb 2017 13:01 Chiara Parravicini < > > chiara.parravic...@guest.unimi.it> wrote: > > > > > Dear Gmx users, > > > > > > using GROMACS version 2016.1, I found the following error in the > > output of > > > the gmx hbond routine: when computed from different groups, where > > one is a > > > subset of the other one, hbonds from the same acceptor/donor pair do > not > > > match. > > > > > > I known that this error has been already widely discussed in previous > > > gromacs versions. Is there any solution? > > > > > > Thanks > > > > > > Chiara > > > > > > > > > > > > -- > > > Chiara Parravicini, PhD > > > Laboratorio di Biochimica e Biofisica Computazionale > > > Dipartimento di Scienze Farmacologiche e Biomolecolari > > > Università degli Studi di Milano > > > Via Balzaretti 9, > > > 20133 Milano, Italy > > > Tel: +39 02-503-18256/18355 > > > Fax: +39 02-503-18284 > > > > > > > > > -- > > > 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. > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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] hbond error
Hi, I just realized that the hbond tool works fine, but produces output in reverse order. The "bug" is in the manual that states: * -hbm: existence matrix for all hydrogen bonds over all frames, this also contains information on solvent insertion into hydrogen bonds. Ordering is identical to that in -hbn index file. Chiara Il 16/02/17 13:41, *Mark Abraham * ha scritto: Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: > Dear Gmx users, > > using GROMACS version 2016.1, I found the following error in the output of > the gmx hbond routine: when computed from different groups, where one is a > subset of the other one, hbonds from the same acceptor/donor pair do not > match. > > I known that this error has been already widely discussed in previous > gromacs versions. Is there any solution? > > Thanks > > Chiara > > > > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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. -- Chiara Parravicini, PhD Laboratorio di Biochimica e Biofisica Computazionale Dipartimento di Scienze Farmacologiche e Biomolecolari Università degli Studi di Milano Via Balzaretti 9, 20133 Milano, Italy Tel: +39 02-503-18256/18355 Fax: +39 02-503-18284 -- 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] hbond error
Hi, I'm not sure whether I properly understand your description of the behaviour. But if you think you have a case where the tool doesn't do what its documentation says, please open an issue at https://redmine.gromacs.org and attach a tarball of files that will help us diagnose and fix it :-) Mark On Thu, 16 Feb 2017 13:01 Chiara Parravicini < chiara.parravic...@guest.unimi.it> wrote: > Dear Gmx users, > > using GROMACS version 2016.1, I found the following error in the output of > the gmx hbond routine: when computed from different groups, where one is a > subset of the other one, hbonds from the same acceptor/donor pair do not > match. > > I known that this error has been already widely discussed in previous > gromacs versions. Is there any solution? > > Thanks > > Chiara > > > > -- > Chiara Parravicini, PhD > Laboratorio di Biochimica e Biofisica Computazionale > Dipartimento di Scienze Farmacologiche e Biomolecolari > Università degli Studi di Milano > Via Balzaretti 9, > 20133 Milano, Italy > Tel: +39 02-503-18256/18355 > Fax: +39 02-503-18284 > > > -- > 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] hbond
On 12/1/16 10:58 AM, Gregory Poon wrote: On 12/1/2016 7:45 AM, Justin Lemkul wrote: On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote: Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online documentation as to how this should be done except a single mention with the -hbm option, which I tried. It generated .xpm files such as the one attached. They open, as far as I can tell, a very vertically compressed plot which I can make nothing out of. Attempts to convert them to eps using xpm2eps output similar results. You can use an .m2p file to adjust the sizes of the x- and y-axes to make it legible. The real value is in the data within, though. You have to map the actual participating groups (the output of of -hbn) with the individual time series in the .xpm from -hbm. So my questions are two-fold: 1) What is happening with the .xpm files? 2) Am I using the correct hbond option to enumerate water-mediated hydrogen bonds? To actually analyze water-mediated H-bonds requires additional work that GROMACS tools don't do. You need to analyze water H-bonds with the two groups of interest separately, then determine if the same water is H-bonded to a moiety in both of those groups in the same frame. This is where tracing the H-bonds in the .xpm file is useful. -Justin Thanks for your comments, Justin. When I invoke hbond by: gmx hbond -f *.xtc -s *.tpr -num -hbn -g (± other options) I get hbnum which shows changes with respect with time, but the hbond.ndx and hbond.log files have no time information. Are they averages of some sort? Or a particular frame that it defaults to? If so, how do I specific the frames/times? Asking for -hbn requires -hbm to be useful. The index file produced is the key for what the hydrogen bonds are in the .xpm file from -hbm. -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] hbond
On 12/1/2016 7:45 AM, Justin Lemkul wrote: On 12/1/16 7:24 AM, Gregory Man Kai Poon wrote: Hi all: I am trying to use hbond in Gromacs 5.1.4 to analyze water-mediated hydrogen bonding between two objects simulated in water. The GROMACS manual discusses this in a Figure (9.8) - "water insertion". There is nothing in the online documentation as to how this should be done except a single mention with the -hbm option, which I tried. It generated .xpm files such as the one attached. They open, as far as I can tell, a very vertically compressed plot which I can make nothing out of. Attempts to convert them to eps using xpm2eps output similar results. You can use an .m2p file to adjust the sizes of the x- and y-axes to make it legible. The real value is in the data within, though. You have to map the actual participating groups (the output of of -hbn) with the individual time series in the .xpm from -hbm. So my questions are two-fold: 1) What is happening with the .xpm files? 2) Am I using the correct hbond option to enumerate water-mediated hydrogen bonds? To actually analyze water-mediated H-bonds requires additional work that GROMACS tools don't do. You need to analyze water H-bonds with the two groups of interest separately, then determine if the same water is H-bonded to a moiety in both of those groups in the same frame. This is where tracing the H-bonds in the .xpm file is useful. -Justin Thanks for your comments, Justin. When I invoke hbond by: gmx hbond -f *.xtc -s *.tpr -num -hbn -g (± other options) I get hbnum which shows changes with respect with time, but the hbond.ndx and hbond.log files have no time information. Are they averages of some sort? Or a particular frame that it defaults to? If so, how do I specific the frames/times? Thanks again, Gregory -- 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] hbond definition in simulations
On 7/19/16 10:07 AM, Joel Markgren wrote: Dear GROMACS users, I have understood that GROMACS has following definition on hydrogen bonds: is a geometric definition, and it states that for a hydrogen bond to be present the donor-hydrogen· · ·acceptor angle is no greater than 30 ◦ and the oxygen-oxygen cut-off distance at most 0.35 nm. But what is the definition, of the bond itself? What I have learned does hydrogen bonds involve stronger forces then regular electrostatics, how does GROMACS formulate the forces involved in hydrogen bonding’s within an simulation. I somehow take it naturally that md simulations do take into account hydrogen bond formations. There is no explicit hydrogen bonding term. GROMACS does nothing special; these interactions are governed almost entirely by the electrostatic terms (partial charges) in the force field. -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] hbond hydroxyl oxygen, both acceptor and donor?
Ah thank you! This fixed the problem. Jeremy Todd First Webb Research Group University of Texas at Austin jeremy_fi...@utexas.edu On Mon, Jul 18, 2016 at 3:31 PM, Justin Lemkul wrote: > > > On 7/18/16 4:27 PM, Jeremy T First wrote: > >> Hello, >> >> I am attempting to quantify the amount of hydrogen bonding environment a >> certain residue experiences during the course of a simulation. To do this, >> I am using gmx hbond to plot the number of hydrogen bonds between the >> solvent (water) and the hydroxyl oxygen of the residue as a function of >> simulation time. >> >> According to the help information for gmx hbond, hydroxyl oxygens are >> classified as hydrogen bond donors. When I select this oxygen and the >> Water >> group in gmx hbond, gromacs finds one less donor than acceptor, leading me >> to believe that the hydroxyl oxygen is classified only as a donor, and not >> also as an acceptor. >> >> Many frames of my simulation show the hydroxyl oxygen (as calculated by >> VMD) donating and accepting a hydrogen bond, but gmx hbond only reports 1 >> hydrogen bond for the frame. >> >> Is there any reason that a hydroxyl oxygen can not simultaneously donate >> and accept a hydrogen bond? If not, is there a way to let gromacs allow >> the >> hydroxyl oxygen to be an acceptor as well? >> >> Any help would be greatly appreciated! >> >> > You can't use just the oxygen atom; the analysis group must contain both O > and H to be considered a donor. If you're just selecting an O and the > entire water group, the O in the hydroxyl can only be considered an > acceptor. > > -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] hbond hydroxyl oxygen, both acceptor and donor?
On 7/18/16 4:27 PM, Jeremy T First wrote: Hello, I am attempting to quantify the amount of hydrogen bonding environment a certain residue experiences during the course of a simulation. To do this, I am using gmx hbond to plot the number of hydrogen bonds between the solvent (water) and the hydroxyl oxygen of the residue as a function of simulation time. According to the help information for gmx hbond, hydroxyl oxygens are classified as hydrogen bond donors. When I select this oxygen and the Water group in gmx hbond, gromacs finds one less donor than acceptor, leading me to believe that the hydroxyl oxygen is classified only as a donor, and not also as an acceptor. Many frames of my simulation show the hydroxyl oxygen (as calculated by VMD) donating and accepting a hydrogen bond, but gmx hbond only reports 1 hydrogen bond for the frame. Is there any reason that a hydroxyl oxygen can not simultaneously donate and accept a hydrogen bond? If not, is there a way to let gromacs allow the hydroxyl oxygen to be an acceptor as well? Any help would be greatly appreciated! You can't use just the oxygen atom; the analysis group must contain both O and H to be considered a donor. If you're just selecting an O and the entire water group, the O in the hydroxyl can only be considered an acceptor. -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] Hbond occupancy
On 7/8/16 9:01 AM, Amali Guruge wrote: Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. You can't get, e.g. % occupancy directly but the gmx hbond output (-hbn -hbm) can be post-processed with a simple script to extract the information. I have a script that does this; contact me off-list if you can't figure it out (it's a good programming exercise :). -Justin On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund wrote: gmx hbond On 8 Jul 2016, at 12:24, Amali Guruge wrote: Dear All, Can anyone know how to calculate H bond occupancy with Gromacs? 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. -- 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] Hbond occupancy
Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund wrote: > gmx hbond > > > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > > > Dear All, > > > > Can anyone know how to calculate H bond occupancy with Gromacs? > > > > 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. > > -- > 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] Hbond occupancy
gmx hbond > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > Dear All, > > Can anyone know how to calculate H bond occupancy with Gromacs? > > 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. -- 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] hbond between backbone atoms
On 6/28/16 6:41 AM, Ming Tang wrote: Dear list, I want to calculate hbond between backbone atoms on different chains of my protein only. but when it give me this error "nothing to be none". I used this command: gxm hbond -f traj.trr -s topol.tpr -num hbnum.xvg -a 30 -r 0.5 I can use this command to get hbond between protein and protein. Can anybody give me some suggestions? Use Mainchain+H. Backbone considers only C+CA+N, so there can be no H-bonds in those atoms. MainChain+H is C+CA+N+H+O, which includes what you actually want. -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] hbond analysis
On 11/4/14 7:26 AM, Urszula Uciechowska wrote: Dear Gromacs users, Regarding the g_hbond analysis. What does exactly represent the second and third column in hbond.xvg file (pasted below)? g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "Hydrogen Bonds" @xaxis label "Time" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" As the legends say, the data presented are hydrogen bonds, and then pairs of atoms that are within the distance criterion but do not satisfy the angle criterion for being a hydrogen bond. -Justin 0 0 0 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 0 0 11 0 0 12 0 0 13 0 0 14 0 0 15 0 0 16 0 0 : Best regrads Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- == 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] hbond analysis
Dear Gromacs users, Regarding the g_hbond analysis. What does exactly represent the second and third column in hbond.xvg file (pasted below)? g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "Hydrogen Bonds" @xaxis label "Time" @yaxis label "Number" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 1 0 0 2 0 0 3 0 0 4 0 0 5 0 0 6 0 0 7 0 0 8 0 0 9 0 0 10 0 0 11 0 0 12 0 0 13 0 0 14 0 0 15 0 0 16 0 0 : Best regrads Urszula University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] hbond analysis
On 10/30/14 7:58 AM, Urszula Uciechowska wrote: Dear gromacs users, I am having some problems with hbond analysis using gromacs. I am interested in hbonds between certain amino acids for example: LYS256 and nucleic acid that has number 2 in my files. I generated the index file which contains r256 and r2 by running make_ndx -f gro -o out.ndx then I run g_hbond g_hbond -f traj.xtc -s .tpr -num hydrogen-bonds-protein.xvg Well, that can't be your command because it doesn't use the index file. Always copy and paste; please don't try to recreate what you did. My xvg file did not contain any hbond between those amino acids, which is not true. I do not know what went wrong. Could anyone suggest me something? Have you verified that the index groups contain what you think they do? What does gmxcheck tell you? Is there any other way to run the hbond? No, there is one program for analyzing hydrogen bonds and it's g_hbond. Is it possible to use the xtc trajectory and run hbond anlysis in ptraj? or can I convert it somehow? It's always possible to convert formats. The question is whether or not you want or need to spend the time doing it. If g_hbond does not detect any hydrogen bonds, either (1) there are none that fit the criteria or (2) your index groups don't correspond to what you think they 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] hbond correspondence between hbond.log and hbmap.xpm
On 6/25/14, 4:04 PM, Zheng Ruan wrote: Hi, I'm new to gromacs and right now I'm trying to use g_hbond to analyze my trajectory. Basically, I create two selections in .ndx file and try to find hydrogen bonds between them. In the output, there is a "y-axis" record in hbond.xpm matrix file. The number of the elements of "y-axis" is the same with those in hbond.log file. I was wondering if they referred to the same thing. That is, if the first row below "y-axis" in hbmap.xpm telling me the hbond interaction of the first interaction in hbond.log file? Or it's the reverse? I'm asking the question because the hydrogen bond reported by g_hbond doesn't seems to be consistent with those found by pymol. The "first" line after the y-axis entry is actually the "last" hydrogen bond listed in hbond.ndx (and maybe the .log file; I've never used that one). The listed H-bonds are read from top-down (in order of increasing atom number) while the matrix should be interpreted as "bottom-up" to correspond to an increasing y-axis. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
