Hi all, Could anyone please refer to me to a paper or other resource that explains in detail (specifically technical) on how to preform g_lie. I know the matter has been brought up here quit often lately but looking through the mailing list archives and reference papaers (Aquist et al. and similar) tend to focus on the theory rather than practice.
Thanks in advance, Gideon 2011/9/12 <gmx-users-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: How do I examine the results didn't write issue (lina) > 2. Re: How do I examine the results didn't write issue (lina) > 3. adding Ca2+ ions to the solvent (either randomly or > restrained) (m r) > 4. g_rms matrix between wt and mutant (Shay Teaching) > 5. Re: g_rms matrix between wt and mutant (Justin A. Lemkul) > 6. Re: g_rms matrix between wt and mutant (Shay Teaching) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Sep 2011 21:10:49 +0800 > From: lina <lina.lastn...@gmail.com> > Subject: Re: [gmx-users] How do I examine the results didn't write > issue > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cag9cjmk-dbt33bowsnt+oik3qyz4n3sozlt6kgvem-z_bfk...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > > lina wrote: > > > >> Hi, > >> > >> I am confused, why the job is running, > >> > >> but they did not write the .edr, .log .xtc ... files. > >> > >> Everything showed so normal, just not writing, > >> > >> when I used thread, all is fine, the writing is normal. > >> > >> just use mpi, I tried different nodes, still not work, now two hours > >> later, still no writing, just running. > >> > >> Thanks for providing any clue for me to examine. > >> > >> > >> > > Sounds like your MPI implementation is broken or you haven't issued the > > command right. If you have a test command that you know should work, run > > that. Otherwise, it's impossible to know if the problem is with Gromacs > or > > something external. If you compiled with threading support, but not MPI > (in > > a separate binary) then MPI will not work on the thread-enabled > executable. > > > > I suspected it's MPI issue, but couple of days ago it's fine, and the > results was able to write. > > I installed both MPI and thread but with different prefix to distinguish. > > Thanks, > > > > > -Justin > > > > -- > > ==============================**========== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==============================**========== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > Best Regards, > > lina > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110912/03f71465/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 12 Sep 2011 21:12:26 +0800 > From: lina <lina.lastn...@gmail.com> > Subject: Re: [gmx-users] How do I examine the results didn't write > issue > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAG9cJm=cx_tYxg4XoqtrXANWXt7rWaTpS6oHWp=ammdrub2...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham <mark.abra...@anu.edu.au > >wrote: > > > On 12/09/2011 10:23 PM, lina wrote: > > > >> Hi, > >> > >> I am confused, why the job is running, > >> > >> but they did not write the .edr, .log .xtc ... files. > >> > >> Everything showed so normal, just not writing, > >> > >> when I used thread, all is fine, the writing is normal. > >> > >> just use mpi, I tried different nodes, still not work, now two hours > >> later, still no writing, just running. > >> > > > > If you can run mdrun_threads -np 4 and get output and your mpirun -np 4 > > mdrun_mpi does not write output, then there must be something wrong with > > your MPI environment. Try another MPI program and see what it does. > > > > I guess I will drop an email to the administrator. > > might be an MPI issue. > > Thanks for your time, > > > > Mark > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > Best Regards, > > lina > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110912/5f715228/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 12 Sep 2011 07:03:19 -0700 (PDT) > From: m r <gmstma_rez...@yahoo.com> > Subject: [gmx-users] adding Ca2+ ions to the solvent (either randomly > or restrained) > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <1315836199.27921.yahoomail...@web34507.mail.mud.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > In an attempt to simulate the effect of adding calcium ion to the solvent > around my protein of interest, I wonder how to add Ca2+ ions in the > following cases (in GROMACS 4.5.4): > > 1) adding Ca2+ ions randomly distributed in the solvent; > > 2) adding Ca2+ such that it is initially restrained in vicinity of some > specified groups on the surface of my protein (I mean: something similar to > restraining the ligand in a search box during its docking to a receptor). > > Any valuable comments are highly appreciated. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110912/9efc28ae/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 12 Sep 2011 17:27:01 +0300 > From: Shay Teaching <shay.teach...@gmail.com> > Subject: [gmx-users] g_rms matrix between wt and mutant > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAG3b_-h2TuTvxwPJ0kYQACxewz+u614j-+dvRh8Fgog=rq1...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > (Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory > and one mutant trajectory using the following command: > > g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n > wt_backbone.ndx > > The file wt_backbone.ndx contains the backbone of the protein (Backbone > indices are identical between wt and mutant). > > The result is that I am getting a well deserved error saying that wt.xtc > and > mutant.xtc has different number of atoms (the tpr itself): > Fatal error: > Second trajectory (76128 atoms) does not match the first one (76129 atoms) > > So the question becomes: Is there a (convenient) way to produce rms-matrix > between wt and mutant? > Or perhaps circumvent this problem in some other way? > I tried looking into g_confrms, but apparently it works only on two frames > instead of trajectories. > > Thanks a lot, > -Shay > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110912/90ec4889/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 12 Sep 2011 10:29:40 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] g_rms matrix between wt and mutant > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e6e1754.7090...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Shay Teaching wrote: > > Hi all, > > (Gromacs 4.0.7): I am trying to make rms matrix between one Wt > > trajectory and one mutant trajectory using the following command: > > > > g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n > > wt_backbone.ndx > > > > The file wt_backbone.ndx contains the backbone of the protein (Backbone > > indices are identical between wt and mutant). > > > > The result is that I am getting a well deserved error saying that wt.xtc > > and mutant.xtc has different number of atoms (the tpr itself): > > Fatal error: > > Second trajectory (76128 atoms) does not match the first one (76129 > atoms) > > > > So the question becomes: Is there a (convenient) way to produce > > rms-matrix between wt and mutant? > > Or perhaps circumvent this problem in some other way? > > Use trjconv to write out new trajectories containing only backbone atoms of > each > protein, then use tpbconv to write a .tpr file with only backbone atoms in > it > (using index groups, if necessary). Then run g_rms again with these new > trajectories and .tpr file. Everything should match if the indices are > chosen > correctly. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Mon, 12 Sep 2011 18:16:08 +0300 > From: Shay Teaching <shay.teach...@gmail.com> > Subject: Re: [gmx-users] g_rms matrix between wt and mutant > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <CAG3b_-iwQdbHg-m9f=2D5Pu19P08yXBed_S7z1TK_5aPft=q...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > When I try to work the command on a small portion of the backbone it seems > to work just fine. But when I try the entire backbone (which is composed of > several *separate* chains) I am getting segmentation fault. > Any workaround for that, so I can use the entire backbone? > Thanks again, > -Shay > > On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > > Shay Teaching wrote: > > > >> Hi all, > >> (Gromacs 4.0.7): I am trying to make rms matrix between one Wt > trajectory > >> and one mutant trajectory using the following command: > >> > >> g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n > >> wt_backbone.ndx > >> > >> The file wt_backbone.ndx contains the backbone of the protein (Backbone > >> indices are identical between wt and mutant). > >> > >> The result is that I am getting a well deserved error saying that wt.xtc > >> and mutant.xtc has different number of atoms (the tpr itself): > >> Fatal error: > >> Second trajectory (76128 atoms) does not match the first one (76129 > atoms) > >> > >> So the question becomes: Is there a (convenient) way to produce > rms-matrix > >> between wt and mutant? > >> Or perhaps circumvent this problem in some other way? > >> > > > > Use trjconv to write out new trajectories containing only backbone atoms > of > > each protein, then use tpbconv to write a .tpr file with only backbone > atoms > > in it (using index groups, if necessary). Then run g_rms again with > these > > new trajectories and .tpr file. Everything should match if the indices > are > > chosen correctly. > > > > -Justin > > > > -- > > ==============================**========== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==============================**========== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110912/96b37352/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 89, Issue 65 > ***************************************** > -- Gideon Lapidoth, MS.c candidate Hemi Gutman Biophysics Lab Department of Biochemistry & Molecular Biology George S. Wise Faculty of Life Sciences Tel Aviv University Israel 69978 <http://ashtoret.tau.ac.il/> Tel: (972-3) 640-9824
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