Re: [gmx-users] PROTEIN FOLDING
Depends. If you're interested in local folding and there are SS motifs in the region you're interested, then yes. If not, no. In terms of overall folding of the entire protein, yes it surely can be an important analysis. J On Wed, Dec 20, 2017 at 1:46 PM, Neha Gupta wrote: > Thank you Joao and Aman. > > I have noted the points you have suggested. > > Do you think analyzing DSSP would help? > > Thanks, > Neha > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > > "You can use various supporting tools from R language to debug your > > trajectory but most third party software support NAMD and charmm format. > > You can use VMD to convert the trajectory to dcd and use R language based > > packages to read your trajectory" > > > > What? How is this useful or helpful? At most it confuses the OP even > more. > > > > Also, the clustering analysis is unlikely to be what you want or need at > > this stage. Why overcomplicate? One of the simplest ways to check that > > there are conformational changes on a given set of atoms is by doing a > RMSD > > analysis using the folded structure as the reference. The RMSD is > somewhat > > degenerate, but should suffice for this purpose. You can use an index > file > > to restrict the RMSD analysis to a particular subset of your system (the > > docking site, for example). > > > > You could look at the radius of gyration as well, Rg, as Aman Deep also > > suggests. This can either be calculated on a subset of atoms or on the > > entire protein. The latter could potentially be used to compare with the > > experimental reference obtained by SAXS, for example. Or you could > > calculate the SAXS curve and get a better understanding of size and shape > > differences between your protein and the reference, but that's more > > advanced stuff. > > > > J > > > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH > > wrote: > > > > > Also you must know, a lot analysis are available over the entire manual > > of > > > Gromacs where all cannot be performed. Gromacs always provide you all > > > necessary analysis but to choose which one is always your choice that > > suits > > > your simulation purpose. > > > > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > > > wrote: > > > > > > > Hi, > > > > > > > > > > > > Thank you for your prompt reply. > > > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > > > "over particular PC sub space" > > > > > > > > Could you please elaborate a bit? > > > > > > > > Thanks a lot once again. > > > > > > > > Thanks, > > > > Neha > > > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH < > drrahulsur...@gmail.com > > > > > > > wrote: > > > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta < > nehaphysic...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > Hi gromacs users, > > > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we > view > > > > > protein > > > > > > folding? > > > > > > > > > > > > How to do it? > > > > > > > > > > > > I want to ascertain if there is any conformation change in > protein > > > > where > > > > > > the ligand binds. Is it possible? > > > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I > want > > to > > > > > make > > > > > > observation through MD simulation which is not obtained through > > > > docking. > > > > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > > > measure > > > > > the structural changes. > > > > > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > > > Thanks, > > > > > > Neha > > > > > > -- > > > > > > 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. > > > > > > > > > > > -- > > > > > *Regards,* > > > > > *Rahul Suresh* > > > > > *Research Scholar* > > > > > *Bharathiar University* > > > > > *Coimbatore* > > > > > -- > > > > > 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
Re: [gmx-users] PROTEIN FOLDING
Thank you Joao and Aman. I have noted the points you have suggested. Do you think analyzing DSSP would help? Thanks, Neha On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "You can use various supporting tools from R language to debug your > trajectory but most third party software support NAMD and charmm format. > You can use VMD to convert the trajectory to dcd and use R language based > packages to read your trajectory" > > What? How is this useful or helpful? At most it confuses the OP even more. > > Also, the clustering analysis is unlikely to be what you want or need at > this stage. Why overcomplicate? One of the simplest ways to check that > there are conformational changes on a given set of atoms is by doing a RMSD > analysis using the folded structure as the reference. The RMSD is somewhat > degenerate, but should suffice for this purpose. You can use an index file > to restrict the RMSD analysis to a particular subset of your system (the > docking site, for example). > > You could look at the radius of gyration as well, Rg, as Aman Deep also > suggests. This can either be calculated on a subset of atoms or on the > entire protein. The latter could potentially be used to compare with the > experimental reference obtained by SAXS, for example. Or you could > calculate the SAXS curve and get a better understanding of size and shape > differences between your protein and the reference, but that's more > advanced stuff. > > J > > On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH > wrote: > > > Also you must know, a lot analysis are available over the entire manual > of > > Gromacs where all cannot be performed. Gromacs always provide you all > > necessary analysis but to choose which one is always your choice that > suits > > your simulation purpose. > > > > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > > wrote: > > > > > Hi, > > > > > > > > > Thank you for your prompt reply. > > > > > > By clustering analysis, are you talking about gmx cluster command? > > > > > > "over particular PC sub space" > > > > > > Could you please elaborate a bit? > > > > > > Thanks a lot once again. > > > > > > Thanks, > > > Neha > > > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > > > wrote: > > > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > > > wrote: > > > > > > > > > Hi gromacs users, > > > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > > protein > > > > > folding? > > > > > > > > > > How to do it? > > > > > > > > > > I want to ascertain if there is any conformation change in protein > > > where > > > > > the ligand binds. Is it possible? > > > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want > to > > > > make > > > > > observation through MD simulation which is not obtained through > > > docking. > > > > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > > measure > > > > the structural changes. > > > > > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > > > Thank you very much in advance. > > > > > > > > > > Thanks, > > > > > Neha > > > > > -- > > > > > 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. > > > > > > > > > -- > > > > *Regards,* > > > > *Rahul Suresh* > > > > *Research Scholar* > > > > *Bharathiar University* > > > > *Coimbatore* > > > > -- > > > > 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. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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/
Re: [gmx-users] Dynamic selection of a shell in a trajectory
Hi, Dynamic selections are implemented, but only for a small subset of GROMACS tools. You can use gmx select to form the appropriate index group, but you'd have to write some other script to get trjconv to pull out individual frames with the matching selection, and then concatenate them into a trajectory file (and decide how you want to deal with the fact that frames may now differ in the number of atoms). Mark On Wed, Dec 20, 2017 at 9:03 PM João Henriques wrote: > Very unlikely and/or impractical. The water selections/analyses you can do > with gromacs' native tools are unfortunately rather limited. From personal > experience I'd suggest trying MDAnalysis or something similar, because it > gives you the freedom to code your our analysis routine with minimal effort > in terms of programming. Plus it allows dynamic selections, which I never > found truly possible with gromacs' native tools. > > J > > > > > On Wed, Dec 20, 2017 at 9:43 AM, Matteo Busato < > busato.mat...@spes.uniud.it> > wrote: > > > Dear all, > > > > > > I'm performing a dynamic of a metal ion in a box consisting of a solvent, > > where the metal is coordinated by six solvent molecules. > > > > I'm writing here because I want to reduce the trajectory including the > > intire box to a trajectory containing only the first coordination shell > of > > the metal, e.g. say to the system "consider a sphere of 8 Angstroms > radius > > from the metal and pick up any residue which has a least one atom inside > > this sphere". In addition, it would be nice to perform a sort of "dynamic > > selection", e.g. if one residue exits and another one enters the sphere I > > want the selection to keep the first one and then the second. > > > > > > Is this possible with Gromacs or do I need to use other tools? I've tryed > > to understand if this was possible with trjconv or gmx select, but I > think > > they're not the right utilities and I couldn't find anyone with this > > problem in a web research. > > > > I would be gratefull if you can help me. > > > > > > Thank you in advance for your answer. > > > > > > Kind regards, > > > > Matteo Busato > > -- > > 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] PROTEIN FOLDING
"You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory" What? How is this useful or helpful? At most it confuses the OP even more. Also, the clustering analysis is unlikely to be what you want or need at this stage. Why overcomplicate? One of the simplest ways to check that there are conformational changes on a given set of atoms is by doing a RMSD analysis using the folded structure as the reference. The RMSD is somewhat degenerate, but should suffice for this purpose. You can use an index file to restrict the RMSD analysis to a particular subset of your system (the docking site, for example). You could look at the radius of gyration as well, Rg, as Aman Deep also suggests. This can either be calculated on a subset of atoms or on the entire protein. The latter could potentially be used to compare with the experimental reference obtained by SAXS, for example. Or you could calculate the SAXS curve and get a better understanding of size and shape differences between your protein and the reference, but that's more advanced stuff. J On Tue, Dec 19, 2017 at 9:52 AM, RAHUL SURESH wrote: > Also you must know, a lot analysis are available over the entire manual of > Gromacs where all cannot be performed. Gromacs always provide you all > necessary analysis but to choose which one is always your choice that suits > your simulation purpose. > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > wrote: > > > Hi, > > > > > > Thank you for your prompt reply. > > > > By clustering analysis, are you talking about gmx cluster command? > > > > "over particular PC sub space" > > > > Could you please elaborate a bit? > > > > Thanks a lot once again. > > > > Thanks, > > Neha > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > wrote: > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > wrote: > > > > > > > Hi gromacs users, > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > protein > > > > folding? > > > > > > > > How to do it? > > > > > > > > I want to ascertain if there is any conformation change in protein > > where > > > > the ligand binds. Is it possible? > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > > make > > > > observation through MD simulation which is not obtained through > > docking. > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > measure > > > the structural changes. > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > Thank you very much in advance. > > > > > > > > Thanks, > > > > Neha > > > > -- > > > > 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. > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > 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. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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-
Re: [gmx-users] Grompp error : Incorrect number of parameters
Hi,
The large energy means your topology is probably broken. Please use a tool
that will write an .itp file for you (e.g. SwissParam?), or next time get
your topology for your ligand working before you try to use it in a
complex. Even get a simple form of the ligand working first, to teach
yourself the process of writing the coordinate file. The more new things
you try to do at once, the less likely you are to fail in ways that you can
help yourself to fix.
Mark
On Wed, Dec 20, 2017 at 8:24 PM RAHUL SURESH
wrote:
> To be included here, the ligand I have uploaded seems to be so congested
> and out of form. Look literally like a clumsy ball.
> I am not sure what make this happen.
>
> On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH
> wrote:
>
> > Dear Alex
> >
> > I have tried that but the system collapse. For em_real.mdp option,I get
> > message stating
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.1#
> >
> > Steepest Descents converged to machine precision in 15 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy = 3.9192084e+11
> > Maximum force = 1.3457252e+14 on atom 629
> > Norm of force = 1.0629695e+12
> >
> > Simulation ended prematurely, no performance report will be written.
> >
> > GROMACS reminds you: "When It Starts to Start It'll Never Stop"
> (Magnapop)
> >
> >
> > On Wed, Dec 20, 2017 at 2:20 PM, Alex wrote:
> >
> >> The description for the Urey-Bradley potential (assuming two quadratic
> >> terms qualify for the proud term "potential") is described in the user
> >> manual, and the constants' order of appearance in the itp file is given
> in
> >> the Table 5.5 of the manual. If you have a basic quadratic angular term
> >> (first term in U-B with two constants) from elsewhere and you want to
> use
> >> it in the U-B format, it is an absolutely trivial task. All you have to
> do
> >> is set the U-B distance-dependent energy component to zero.
> >>
> >> Alex
> >>
> >>
> >>
> >> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
> >>
> >>> Hi
> >>>
> >>> Thank you Mark.
> >>>
> >>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> >>> >
> >>> wrote:
> >>>
> >>> Hi,
>
> Sorry I don't know how any of these non-GROMACS tools work, or even
> whether
> they actually generate Urey Bradley interactions that have all the
> terms. I
> suggest you spend some time with the documentation.
>
> Mark
>
> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH
> wrote:
>
> Sorry Mark, I failed to note that.
> >
> > I am afraid that I don't know what that are those components and how
> > and
> > where to find it. If you are actually meaning about "ub0 kub"
> >
> components,
>
> > how could i find the value for it. In case of swiss param generated
> itp
> > file, these components appear to be 0. Any help here please?
> >
> >
> > On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
> > mark.j.abra...@gmail.com
> >
> > wrote:
> >
> > Hi,
> >>
> >> Please read my answer.
> >>
> >> Mark
> >>
> >> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH >
> >> wrote:
> >>
> >> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul
> >>>
> >> wrote:
>
> >
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
>
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> > Incorrect number of parameters - found 2, expected 4 or 8 for
> >
> U-B.
> >
> >> My itp file as follows
> >
> > [ angles ]
> >
> > 1 2 29 579.178 109.588 *{Line 89}*
> > 1 2 3 532.192 112.817
> > 2 3 31 551.424 109.189
> >
> > From the manual chapter 5, function of U-B is 5. And it works
> >
> fine
>
> > for
> >>
> >>> function type 2 and 8.
> >
> > Any thing better could be done?
> >
> As the error tells you, the U-B functional form requires at least
> 4
> para
Re: [gmx-users] Measuring distance to the nearest image
Hi, From its help: "gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc." You've got it computing distances within each group, which is why they have little or no variation and have the length of a C-H bond and maybe a C-C bond. Per "gmx help selections examples", you might try something like "gmx distance -select 'com of HYP1 plus com of GLPInt1' -s -n" I'll add an explicit tip to the help text - you're not the first person to assume that giving it two selection groups gets some kind of distance between the groups. Mark On Wed, Dec 20, 2017 at 7:56 PM Anthony Nash wrote: > Hi Mark, > > I think with a combined project list as long as my arm and going between > VMD and Gromacs that the fault lies with me. A misunderstanding with the > decimal point. However, I am a little confused over the output and despite > reading the help I am still none the wiser. > > I go on to select two groups: > > [ HYP1 ] ← part of the side chain of a hydroxyproline > 4669 4670 4672 4673 4676 4677 > [ GLPInt1 ] ← > 563 564 566 567 570 571 574 576 > > I assume the average absolute distance between the two groups will be the > same regardless of which one you take your measurement (as x1, y1, z1) > from. My output looks like: > > @title "Average distance" > @xaxis label "Time (ps)" > @yaxis label "Distance (nm)" > @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 "HYP1" > @ s1 legend "GLPInt1" > 1.0000.1090.159 > 1.2000.1090.159 > 1.4000.1090.160 > > Reflected in the on-screen output (I have just used a tiny sample size to > run this very quickly, the standard deviation in the larger sample size is > much different) > > Analyzed 501 frames, last time 100.200 > HYP1: > Number of samples: 1503 > Average distance: 0.10900 nm > Standard deviation: 0.0 nm > GLPInt1: > Number of samples: 2004 > Average distance: 0.15911 nm > Standard deviation: 0.05431 nm > > I want the distance between HYP1 and GLPInt1. Why the two measurements? > Clearly there is something I do not understand about the gmx distance > command. > > Really hope you can clear this up. Thanks again! > Anthony > > > On 19/12/2017 11:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mark Abraham" < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > mark.j.abra...@gmail.com> wrote: > > Hi, > > An example where the structure comes from a single frame would be a > useful > thing to explore whether the code is working correctly. I don't think > the > composition of the index groups should matter, but I can't see how the > code > wouldn't work correctly. > > Mark > > On Tue, Dec 19, 2017, 10:12 PM Anthony Nash < > anthony.n...@dpag.ox.ac.uk> > wrote: > > > Hi Mark, > > > > As an example, from numerous attempts, I have tried: > > > > /usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 1 -f > > crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx > > > > which was throwing a value of around 8 nm, rather than the 2 nm I was > > expecting if it took a measurement from over the periodic boundary. > > > > Unfortunately, I’ve left the necessary harddrive at home. I’’’ be > more > > than happy to respond with a more comprehensive example along with > output > > data in a few hours. > > > > Thanks > > Anthony > > > > > > On 19/12/2017 11:02, " > gromacs.org_gmx-users-boun...@maillist.sys.kth.se > > on behalf of Mark Abraham" < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > > mark.j.abra...@gmail.com> wrote: > > > > Hi > > > > This is exactly what two well chosen selections should produce, > given > > a tpr > > and the PBC option. What have you tried that didn't work as you > > expected? > > > > Mark > > > > On Mon, Dec 18, 2017, 5:23 PM Anthony Nash < > anthony.n...@dpag.ox.ac.uk > > > > > wrote: > > > > > > > > Hi all, > > > > > > I am trying to measure the distance between the COM of two > side chain > > > functional groups across the periodic boundary to their > nearest image > > > rather than across the unit cell itself. I have tried several > gromacs > > > distance commands with no success and more at random as I trawl > > through the > > > help and manual, so I won’t replicate those commands here. > > > > > > This link is a hand drawn image of what I am trying to do. I > would > > like to > > > measure how far apart the two
Re: [gmx-users] Dynamic selection of a shell in a trajectory
Very unlikely and/or impractical. The water selections/analyses you can do with gromacs' native tools are unfortunately rather limited. From personal experience I'd suggest trying MDAnalysis or something similar, because it gives you the freedom to code your our analysis routine with minimal effort in terms of programming. Plus it allows dynamic selections, which I never found truly possible with gromacs' native tools. J On Wed, Dec 20, 2017 at 9:43 AM, Matteo Busato wrote: > Dear all, > > > I'm performing a dynamic of a metal ion in a box consisting of a solvent, > where the metal is coordinated by six solvent molecules. > > I'm writing here because I want to reduce the trajectory including the > intire box to a trajectory containing only the first coordination shell of > the metal, e.g. say to the system "consider a sphere of 8 Angstroms radius > from the metal and pick up any residue which has a least one atom inside > this sphere". In addition, it would be nice to perform a sort of "dynamic > selection", e.g. if one residue exits and another one enters the sphere I > want the selection to keep the first one and then the second. > > > Is this possible with Gromacs or do I need to use other tools? I've tryed > to understand if this was possible with trjconv or gmx select, but I think > they're not the right utilities and I couldn't find anyone with this > problem in a web research. > > I would be gratefull if you can help me. > > > Thank you in advance for your answer. > > > Kind regards, > > Matteo Busato > -- > 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] Grompp error : Incorrect number of parameters
To be included here, the ligand I have uploaded seems to be so congested
and out of form. Look literally like a clumsy ball.
I am not sure what make this happen.
On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH
wrote:
> Dear Alex
>
> I have tried that but the system collapse. For em_real.mdp option,I get
> message stating
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.1#
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = 3.9192084e+11
> Maximum force = 1.3457252e+14 on atom 629
> Norm of force = 1.0629695e+12
>
> Simulation ended prematurely, no performance report will be written.
>
> GROMACS reminds you: "When It Starts to Start It'll Never Stop" (Magnapop)
>
>
> On Wed, Dec 20, 2017 at 2:20 PM, Alex wrote:
>
>> The description for the Urey-Bradley potential (assuming two quadratic
>> terms qualify for the proud term "potential") is described in the user
>> manual, and the constants' order of appearance in the itp file is given in
>> the Table 5.5 of the manual. If you have a basic quadratic angular term
>> (first term in U-B with two constants) from elsewhere and you want to use
>> it in the U-B format, it is an absolutely trivial task. All you have to do
>> is set the U-B distance-dependent energy component to zero.
>>
>> Alex
>>
>>
>>
>> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
>>
>>> Hi
>>>
>>> Thank you Mark.
>>>
>>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham >> >
>>> wrote:
>>>
>>> Hi,
Sorry I don't know how any of these non-GROMACS tools work, or even
whether
they actually generate Urey Bradley interactions that have all the
terms. I
suggest you spend some time with the documentation.
Mark
On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH
wrote:
Sorry Mark, I failed to note that.
>
> I am afraid that I don't know what that are those components and how
> and
> where to find it. If you are actually meaning about "ub0 kub"
>
components,
> how could i find the value for it. In case of swiss param generated itp
> file, these components appear to be 0. Any help here please?
>
>
> On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
> mark.j.abra...@gmail.com
>
> wrote:
>
> Hi,
>>
>> Please read my answer.
>>
>> Mark
>>
>> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
>> wrote:
>>
>> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul
>>>
>> wrote:
>
On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> Dear all
>
> For grompp em.mdp I get an error
>
> ERROR 1 [file THC.itp, line 89]:
> Incorrect number of parameters - found 2, expected 4 or 8 for
>
U-B.
>
>> My itp file as follows
>
> [ angles ]
>
> 1 2 29 579.178 109.588 *{Line 89}*
> 1 2 3 532.192 112.817
> 2 3 31 551.424 109.189
>
> From the manual chapter 5, function of U-B is 5. And it works
>
fine
> for
>>
>>> function type 2 and 8.
>
> Any thing better could be done?
>
As the error tells you, the U-B functional form requires at least 4
parameters; look at its functional form. See Table 5.5.
>>>
>>> Dear Justin
>>>
>>> But the parameter obtained from ffTK have only two. What could be
>>>
>> done.?
>
>>
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support
Re: [gmx-users] Grompp error : Incorrect number of parameters
Dear Alex
I have tried that but the system collapse. For em_real.mdp option,I get
message stating
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 3.9192084e+11
Maximum force = 1.3457252e+14 on atom 629
Norm of force = 1.0629695e+12
Simulation ended prematurely, no performance report will be written.
GROMACS reminds you: "When It Starts to Start It'll Never Stop" (Magnapop)
On Wed, Dec 20, 2017 at 2:20 PM, Alex wrote:
> The description for the Urey-Bradley potential (assuming two quadratic
> terms qualify for the proud term "potential") is described in the user
> manual, and the constants' order of appearance in the itp file is given in
> the Table 5.5 of the manual. If you have a basic quadratic angular term
> (first term in U-B with two constants) from elsewhere and you want to use
> it in the U-B format, it is an absolutely trivial task. All you have to do
> is set the U-B distance-dependent energy component to zero.
>
> Alex
>
>
>
> On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
>
>> Hi
>>
>> Thank you Mark.
>>
>> On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham
>> wrote:
>>
>> Hi,
>>>
>>> Sorry I don't know how any of these non-GROMACS tools work, or even
>>> whether
>>> they actually generate Urey Bradley interactions that have all the
>>> terms. I
>>> suggest you spend some time with the documentation.
>>>
>>> Mark
>>>
>>> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH
>>> wrote:
>>>
>>> Sorry Mark, I failed to note that.
I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub"
>>> components,
>>>
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?
On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <
mark.j.abra...@gmail.com
wrote:
Hi,
>
> Please read my answer.
>
> Mark
>
> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
> wrote:
>
> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul
>>
> wrote:
>>>
>>> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
>>>
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for
>>> U-B.
> My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 109.189
From the manual chapter 5, function of U-B is 5. And it works
>>> fine
>>>
for
>
>> function type 2 and 8.
Any thing better could be done?
>>> As the error tells you, the U-B functional form requires at least 4
>>> parameters; look at its functional form. See Table 5.5.
>>>
>>
>> Dear Justin
>>
>> But the parameter obtained from ffTK have only two. What could be
>>
> done.?
>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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.
>>>
>>> --
>> *Regards,*
>> *Rahul Suresh*
>> *Research Schol
Re: [gmx-users] Measuring distance to the nearest image
Hi Mark, I think with a combined project list as long as my arm and going between VMD and Gromacs that the fault lies with me. A misunderstanding with the decimal point. However, I am a little confused over the output and despite reading the help I am still none the wiser. I go on to select two groups: [ HYP1 ] ← part of the side chain of a hydroxyproline 4669 4670 4672 4673 4676 4677 [ GLPInt1 ] ← 563 564 566 567 570 571 574 576 I assume the average absolute distance between the two groups will be the same regardless of which one you take your measurement (as x1, y1, z1) from. My output looks like: @title "Average distance" @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @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 "HYP1" @ s1 legend "GLPInt1" 1.0000.1090.159 1.2000.1090.159 1.4000.1090.160 Reflected in the on-screen output (I have just used a tiny sample size to run this very quickly, the standard deviation in the larger sample size is much different) Analyzed 501 frames, last time 100.200 HYP1: Number of samples: 1503 Average distance: 0.10900 nm Standard deviation: 0.0 nm GLPInt1: Number of samples: 2004 Average distance: 0.15911 nm Standard deviation: 0.05431 nm I want the distance between HYP1 and GLPInt1. Why the two measurements? Clearly there is something I do not understand about the gmx distance command. Really hope you can clear this up. Thanks again! Anthony On 19/12/2017 11:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" wrote: Hi, An example where the structure comes from a single frame would be a useful thing to explore whether the code is working correctly. I don't think the composition of the index groups should matter, but I can't see how the code wouldn't work correctly. Mark On Tue, Dec 19, 2017, 10:12 PM Anthony Nash wrote: > Hi Mark, > > As an example, from numerous attempts, I have tried: > > /usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 1 -f > crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx > > which was throwing a value of around 8 nm, rather than the 2 nm I was > expecting if it took a measurement from over the periodic boundary. > > Unfortunately, I’ve left the necessary harddrive at home. I’’’ be more > than happy to respond with a more comprehensive example along with output > data in a few hours. > > Thanks > Anthony > > > On 19/12/2017 11:02, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mark Abraham" < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > mark.j.abra...@gmail.com> wrote: > > Hi > > This is exactly what two well chosen selections should produce, given > a tpr > and the PBC option. What have you tried that didn't work as you > expected? > > Mark > > On Mon, Dec 18, 2017, 5:23 PM Anthony Nash > > wrote: > > > > > Hi all, > > > > I am trying to measure the distance between the COM of two side chain > > functional groups across the periodic boundary to their nearest image > > rather than across the unit cell itself. I have tried several gromacs > > distance commands with no success and more at random as I trawl > through the > > help and manual, so I won’t replicate those commands here. > > > > This link is a hand drawn image of what I am trying to do. I would > like to > > measure how far apart the two large dots are across the periodic > boundary. > > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as > it > > takes the measurement from within the unit cell. > > > > > > > https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg > > If this involve a tcl script in VMD I would appreciate knowing how > to code > > for an atom selection in a “Periodic” image rather than the “Self”. > > > > Loads of thanks! > > Anthony > > -- > > 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
Re: [gmx-users] Grompp error : Incorrect number of parameters
The description for the Urey-Bradley potential (assuming two quadratic
terms qualify for the proud term "potential") is described in the user
manual, and the constants' order of appearance in the itp file is given
in the Table 5.5 of the manual. If you have a basic quadratic angular
term (first term in U-B with two constants) from elsewhere and you want
to use it in the U-B format, it is an absolutely trivial task. All you
have to do is set the U-B distance-dependent energy component to zero.
Alex
On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
Hi
Thank you Mark.
On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham
wrote:
Hi,
Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.
Mark
On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH
wrote:
Sorry Mark, I failed to note that.
I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub"
components,
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?
On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham
Hi,
Please read my answer.
Mark
On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
wrote:
On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul
wrote:
On 12/19/17 11:14 AM, RAHUL SURESH wrote:
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for
U-B.
My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 109.189
From the manual chapter 5, function of U-B is 5. And it works
fine
for
function type 2 and 8.
Any thing better could be done?
As the error tells you, the U-B functional form requires at least 4
parameters; look at its functional form. See Table 5.5.
Dear Justin
But the parameter obtained from ffTK have only two. What could be
done.?
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
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.
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
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or
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Support/Mailing_Lists/GMX-Users_List before posting!
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* 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.
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
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send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Dynamic selection of a shell in a trajectory
Dear all, I'm performing a dynamic of a metal ion in a box consisting of a solvent, where the metal is coordinated by six solvent molecules. I'm writing here because I want to reduce the trajectory including the intire box to a trajectory containing only the first coordination shell of the metal, e.g. say to the system "consider a sphere of 8 Angstroms radius from the metal and pick up any residue which has a least one atom inside this sphere". In addition, it would be nice to perform a sort of "dynamic selection", e.g. if one residue exits and another one enters the sphere I want the selection to keep the first one and then the second. Is this possible with Gromacs or do I need to use other tools? I've tryed to understand if this was possible with trjconv or gmx select, but I think they're not the right utilities and I couldn't find anyone with this problem in a web research. I would be gratefull if you can help me. Thank you in advance for your answer. Kind regards, Matteo Busato -- 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.
