I have tried -pbc nojump, and other options given in that link but still my protein gets jumped! Plz guide me, how to stop this ? --------------------- orig.Message --------------------- From : gmx-users-requ...@gromacs.org To : gmx-users@gromacs.org Sent date : 2013-02-14 18:42 Subject : gmx-users Digest, Vol 106, Issue 72 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. scattering vector analysis (Rajalakshmi.C) 2. RE: Stopping protein jumping inside box? (vivek modi) 3. Resuming of the trajectory calculation (James Starlight) 4. Re: Whether CHARMM force field in GROMACS is different from that in CHARMM commercial package (David van der Spoel) 5. Re: Resuming of the trajectory calculation (Felipe Pineda, PhD) 6. Re: Resuming of the trajectory calculation (James Starlight) 7. Re: Resuming of the trajectory calculation (Felipe Pineda, PhD) 8. Number of interactions per residue (Kavyashree M) ---------------------------------------------------------------------- Message: 1 Date: Thu, 14 Feb 2013 12:00:26 +0530 From: "Rajalakshmi.C" <ch11d...@smail.iitm.ac.in> Subject: [gmx-users] scattering vector analysis To: gmx-users@gromacs.org Message-ID: <20130214062054.m45...@smail.iitm.ac.in> Content-Type: text/plain; charset=utf-8 hi all, i have done scattering function analysis using g_rdf command for polymer-solvent system. i got the plot of scattering vector q(1/nm) vs intensity .now i want to convert the scattering vector (q) value in to distance i.e. 'd' the fundamental polymer books have the relation for light scattering, that relation is lamda= 2*d*sin(theta). this theta value can be obtained from q.can anybody tell, what type of scattering gromacs use to calculate q . and what is the relation to convert scattering vector q to distance d for that particular scattering type which gromacs using thanks in advance. -- Open WebMail Project (http://openwebmail.org) ------------------------------ Message: 2 Date: Thu, 14 Feb 2013 12:19:15 +0530 From: vivek modi <modi.vivek2...@gmail.com> Subject: [gmx-users] RE: Stopping protein jumping inside box? To: gmx-users@gromacs.org Message-ID: <CADiSEiBymb77Bej-yU3TaUjk_tcGYr6bz1fQTnL-=hrfd18...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 > > Message: 1 > Date: Thu, 14 Feb 2013 14:13:03 +0900 (KST) > From: ????? <ra...@kaist.ac.kr> > Subject: [gmx-users] RE: Stopping protein jumping inside box? > To: gmx-users@gromacs.org, gmx-users-requ...@gromacs.org > Message-ID: <511c745f3fe9_@_imoxion.com> > Content-Type: text/plain; charset="UTF-8" > > Dear gmx, > > I've used -pbc nojump options but still the protein goes all around the box > within 4ns. Any specific command to avoid this ? It's a myoglobin protein! Try this command. http://www.mail-archive.com/gmx-users@gromacs.org/msg13353.html Regards, -Vivek > --------------------- orig.Message --------------------- > >From : gmx-users-requ...@gromacs.org > To : gmx-users@gromacs.org > Sent date : 2013-02-14 07:24 > Subject : gmx-users Digest, Vol 106, Issue 69 > 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. Stopping protein jumping inside box (?????) > 2. Re: Stopping protein jumping inside box (Naga Sundar) > 3. Re: Stopping protein jumping inside box (Justin Lemkul) > 4. RE: on the ussage of SD1 integrator (Berk Hess) > 5. Chandler autcorrelation function fitting (KARAKAS Esra) > 6. Bond potential of atom groups (Steven Neumann) > 7. Join my network on LinkedIn (Gideon Lapidoth via LinkedIn) > 8. GROMOS54A8 parameters in GROMACS format (ABEL Stephane 175950) > 9. Re: different springs - WHAM (Steven Neumann) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Feb 2013 22:29:05 +0900 (KST) > From: ????? <ra...@kaist.ac.kr> > Subject: [gmx-users] Stopping protein jumping inside box > To: gmx-users@gromacs.org > Message-ID: <511b98243fa7_@_imoxion.com> > Content-Type: text/plain; charset="utf-8" > > Dear gmx users, > > > I need to stop my protein jumping inside box. I have used -pbc mol -ur > compact -center command too but still the protein gets moving from one place > to other. > > > Could you please suggest me how to make the protein to stop in one place ? > Moreover, its protein with their ligand. > > > > > Thnx. > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Feb 2013 05:47:07 -0800 > From: Naga Sundar <naga25sun...@gmail.com> > Subject: Re: [gmx-users] Stopping protein jumping inside box > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <calobx4n_6huojhv-aecjgj9uctvivv2h5u-+izyvizmr0ec...@mail.gmail.com> > Content-Type: text/plain; charset=EUC-KR > > Hi > Plz try -pbc nojump option...It may work > > On Wed, Feb 13, 2013 at 5:29 AM, ������������������������������ > <ra...@kaist.ac.kr> wrote: > >> Dear gmx users, >> >> >> I need to stop my protein jumping inside box. I have used -pbc mol -ur >> compact -center command too but still the protein gets moving from one >> place to other. >> >> >> Could you please suggest me how to make the protein to stop in one place ? >> Moreover, its protein with their ligand. >> >> >> >> >> Thnx. >> >> >> >> -- >> 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! >> * 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 >> > > > > -- > Regards > N.NagaSundaram > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Feb 2013 08:50:04 -0500 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Stopping protein jumping inside box > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <511b9a0...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 2/13/13 8:47 AM, Naga Sundar wrote: >> Hi >> Plz try -pbc nojump option...It may work >> > > Several iterations of trjconv are often needed to achieve the desired > representation. Indeed, the first step to removing jumps should be -pbc > nojump...which removes jumps ;) > > -Justin > >> On Wed, Feb 13, 2013 at 5:29 AM, >> ��������������������������������������������� <ra...@kaist.ac.kr> wrote: >> >>> Dear gmx users, >>> >>> >>> I need to stop my protein jumping inside box. I have used -pbc mol -ur >>> compact -center command too but still the protein gets moving from one >>> place to other. >>> >>> >>> Could you please suggest me how to make the protein to stop in one place ? >>> Moreover, its protein with their ligand. >>> >>> >>> >>> >>> Thnx. >>> >>> >>> >>> -- >>> 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! >>> * 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 >>> >> >> >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > ------------------------------ Message: 3 Date: Thu, 14 Feb 2013 10:13:49 +0300 From: James Starlight <jmsstarli...@gmail.com> Subject: [gmx-users] Resuming of the trajectory calculation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CAALQopy8k6gpa_4jF5jW2Moo3=fcv47ecnvlc1g24zjhmpp...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Gromacs Users! I have completed 100ns md trajectory. I 'd like to go on that simulation adding extra 100 ns to the existing trajectory (with appending of both trajectories in single file during that simulation) If I do it just via mdrun -v -cpi md -deffnm md the simulation have not gone on because the simulation time defined in mdp file was over. on contrary if I define new mdp file via grompt the second trajectory save in the another file Does it possible to continue simulation in the existing file? James ------------------------------ Message: 4 Date: Thu, 14 Feb 2013 08:17:24 +0100 From: David van der Spoel <sp...@xray.bmc.uu.se> Subject: Re: [gmx-users] Whether CHARMM force field in GROMACS is different from that in CHARMM commercial package To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511c8f84.1090...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2013-02-14 07:02, fayaz wrote: > Dear Gromacs Forum, > > I want to do RNA simulation using Gromacs. I have installed gromacs 4.5.5 > and i found Charmm force field present in it. Can I use this force field for > my simulation. I am asking this because I heard that Charmm force field in > Gromacs is incomplete and different from the one that is present in CHARMM > software package. I think this conception is present with many of the > gromacs users. Most of my friends are also not using Charmm force field that > comes with gromacs. Please clear this doubt. > Please read the paper by Bjelkmar et al. about the implementation of the FF. Rumors is not enough, but if there is concrete evidence that something is incorrect a bug-report should be filed at http://redmine.gromacs.org. Another question is whether Amber or Charmm is the better force field for RNA. In my group we use Amber. > Thanks in advance > > Fayaz > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/Whether-CHARMM-force-field-in-GROMACS-is-different-from-that-in-CHARMM-commercial-package-tp5005524.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------ Message: 5 Date: Thu, 14 Feb 2013 09:22:16 +0100 From: "Felipe Pineda, PhD" <luis.pinedadecas...@lnu.se> Subject: Re: [gmx-users] Resuming of the trajectory calculation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511c9eb8.4000...@lnu.se> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Very frequently it helps just to do some searches by your own and read _carefully_ the documentation: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend On 02/14/2013 08:13 AM, James Starlight wrote: > Dear Gromacs Users! > > I have completed 100ns md trajectory. > > I 'd like to go on that simulation adding extra 100 ns to the existing > trajectory (with appending of both trajectories in single file during > that simulation) > > If I do it just via > > mdrun -v -cpi md -deffnm md > the simulation have not gone on because the simulation time defined in > mdp file was over. > > > on contrary if I define new mdp file via grompt the second trajectory > save in the another file > > > Does it possible to continue simulation in the existing file? > > James ------------------------------ Message: 6 Date: Thu, 14 Feb 2013 12:11:33 +0300 From: James Starlight <jmsstarli...@gmail.com> Subject: Re: [gmx-users] Resuming of the trajectory calculation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <caalqopz_8fcrwkc55dyrhmwdjzhf5f4bauwimtahffdvr0k...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I've already tried to do it in accordance to that instructions! firstly I've created new tpr file where I changed only duration of my simulation grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr then I've launched mdrun mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append where old is the name of all files from old simulation. after this mdrun produced new set of all files and backuped (to the #old) previous files. But I want to extend simuklation in my existing files. James 2013/2/14 Felipe Pineda, PhD <luis.pinedadecas...@lnu.se>: > Very frequently it helps just to do some searches by your own and read > _carefully_ the documentation: > > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend > > > On 02/14/2013 08:13 AM, James Starlight wrote: >> >> Dear Gromacs Users! >> >> I have completed 100ns md trajectory. >> >> I 'd like to go on that simulation adding extra 100 ns to the existing >> trajectory (with appending of both trajectories in single file during >> that simulation) >> >> If I do it just via >> >> mdrun -v -cpi md -deffnm md >> the simulation have not gone on because the simulation time defined in >> mdp file was over. >> >> >> on contrary if I define new mdp file via grompt the second trajectory >> save in the another file >> >> >> Does it possible to continue simulation in the existing file? >> >> James > > > -- > 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! > * 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 ------------------------------ Message: 7 Date: Thu, 14 Feb 2013 10:17:57 +0100 From: "Felipe Pineda, PhD" <luis.pinedadecas...@lnu.se> Subject: Re: [gmx-users] Resuming of the trajectory calculation To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <511cabc5.9030...@lnu.se> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed It's all about comprehending reading. If you look carefully at the documentation again, you will find: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt What it's the right thing to do. On 02/14/2013 10:11 AM, James Starlight wrote: > I've already tried to do it in accordance to that instructions! > > > firstly I've created new tpr file where I changed only duration of my > simulation > grompp -f ./mdps/md_sd.mdp -n index -c old.tpr -o new.tpr > > then I've launched mdrun > > mdrun -v -s new.tpr -cpi old.cpi -deffnm old -append > > where old is the name of all files from old simulation. > > after this mdrun produced new set of all files and backuped (to the > #old) previous files. But I want to extend simuklation in my existing > files. > > James > ------------------------------ Message: 8 Date: Thu, 14 Feb 2013 15:12:13 +0530 From: Kavyashree M <hmkv...@gmail.com> Subject: [gmx-users] Number of interactions per residue To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <caplgqjp-kywbdwwf2vjczawxncs7q3mutywgkbjwnwuoj0x...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear users, How can I get the number of interactions of each residue within a cut off as a function of time. just like g_saltbr writes with the option -sep. I tried using g_mdmat but it gives an average contact map. Thank you Kavya ------------------------------ -- 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 106, Issue 72 ******************************************
-- 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! * 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