Hi Nicholas, Sorry, I wrote the bead names wrong in the mail. I have just used the correct CG names, but could not see any bond other than one.
Thank you On Thu, Dec 3, 2009 at 11:56 AM, <gmx-users-requ...@gromacs.org> wrote: > 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: Pressure annealing in Gromacs? (Jussi Lehtola) > 2. RE: Exclusions in topology file seem not working for big > systems (Berk Hess) > 3. "coarse_grain.tcl" script does not show all of the > coarse-grained bonds in vmd (Ozge Engin) > 4. Re: "coarse_grain.tcl" script does not show all of the > coarse-grained bonds in vmd (Nicolas Sapay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 03 Dec 2009 09:22:46 +0200 > From: Jussi Lehtola <jussi.leht...@helsinki.fi> > Subject: Re: [gmx-users] Pressure annealing in Gromacs? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <1259824966.1913.1.ca...@politzer.theorphys.helsinki.fi> > Content-Type: text/plain; charset="UTF-8" > > On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: > > Jussi Lehtola wrote: > > > I'm experiencing trouble converging the density of some heavy liquid > > > alcohols (after 10 ns of simulation the density is still changing > > > linearly). Is there any way to run pressure annealing in Gromacs? > > > Running the system through a high pressure and temperature might give > an > > > equilibrium structure quicker. > > > > There's nothing native that I'm aware of, but it should be > > straightforward to use sed or perl in a script to do the annealing "by > > hand" in a series of mdrun invocations. > > Yup, that came to mind but then one ends up with N trajectories and log > files. And one has to run a big pile of grompp commands, that waste some > parallel run time, so I really would like something integrated. > > Besides, a thing like changing the reference pressure should be a > no-brainer in the source code - assuming the code is well structured and > one knows it well beforehand. > > Anyway, the problem was solved for now already. Still, pressure > annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla > about it.) > > -- > ------------------------------------------------------ > Jussi Lehtola, FM, Tohtorikoulutettava > Fysiikan laitos, Helsingin Yliopisto > jussi.leht...@helsinki.fi, p. 191 50632 > ------------------------------------------------------ > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > jussi.leht...@helsinki.fi > ------------------------------------------------------ > > > > > ------------------------------ > > Message: 2 > Date: Thu, 3 Dec 2009 09:30:27 +0100 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] Exclusions in topology file seem not working > for big systems > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <col113-w6464fde0d2532eb97fca938e...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > If you really had too many exclusions you would get an error message. > > So I just tested this. > I used the couple_moltype option to couple a 389 atom protein. > This generates exclusions between each protein atom and the 388 others. > All interactions are excluded correctly (and re-added as special 1-4's > because > of the couple option). > So I don't understand what is going wrong in your case. > > Berk > > Date: Wed, 2 Dec 2009 09:31:03 -0800 > From: resa...@yahoo.com > Subject: Re: [gmx-users] Exclusions in topology file seem not working for > big systems > To: gmx-users@gromacs.org > > > > Thanks for your response Dr van der Spoel. > > Then there is a limit on the number of atoms that can be defined in the > exclusions section. My smaller system has 60 atoms and I used exclusions > successfully for that, so I guess the limit might be a little more than 32. > > Regarding the use of energygrp_excl,it seems it does not work with PME. If > I define the protein in the energygrp_excl group, grompp gives me this > warning: > Can not exclude the lattice Coulomb energy between energy groups > > Which I think means some of electrostatics is not going to be excluded > between protein atoms. Is there a workaround for this? I think my last > resort would be to run a simulation first with PME and without exclusions, > and then rerunning it but this time by defining protein in the > energygrp_excl and using cut-off instead of PME. Then I guess I will be > left with only protein-water interactions. > > Regards, > Reza Salari > > > From: David van der Spoel <sp...@xray.bmc.uu.se> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Wed, December 2, 2009 11:59:49 AM > Subject: Re: [gmx-users] Exclusions in topology file seem not working for > big systems > > > Reza Salari wrote: > > Hi All, > > > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I need it to be > frozen).¨ > > You can have max 32 exclusions per atom AFAIK. > However you can use energy_group_excluisions in the mdp file. > > > > To calculate the desolvation energy, I need to exclude all the > non-bonding interactions among protein atoms, then the dA that I get > corresponds to the desolvation energy (and doesn't include the lost > interactions between mutated residue and the rest of protein). I couldn't > use energygrp_excl in mdp file since I am using PME. So I defined > exclusions in topology file as follows (three-dot means > that numbers continue to the last number): > > > > [ exclusions] > > 1 2 3 4 5 6 ... 6420 > > 2 1 3 4 5 6 ... 6420 > > 3 1 2 4 5 6 ... 6420 > > ... > > ... > > 6420 1 2 3 ... 6419 > > > > I used gmxdump to check that the exclusions were actually implemented, > and it seems that they were. > > > > However when I use g_energy, I don't get zero energy for short range > interactions. Here are the results of g_energy for simulations with and > without exclusions: > > > > Coul-SR:Protein-Protein LJ-SR:Protein-Protein > Coul-14:Protein-Protein LJ-14:Protein-Protein > > no exclusions -20277.6 > -13030.7 37023.9 > 7890.52 > > using exclusions -16221.2 > -10332.9 > 37023.9 > 7890.52 > > > > > > I did the same test with a small system (~6 residue) and I did get zero > SR interactions. While the exclusions work for my small system, I don't know > why they seem not working for my bigger system. Am I missing something here > or is there something like an implicit limit for the number of atoms that > can be defined in the exclusion section of topology file? > > > > I appreciate any hint or help. > > > > Regards, > > Reza Salari > > > > > -- David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 > 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > -- 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/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/mailing_lists/users.php > > > > _________________________________________________________________ > New Windows 7: Find the right PC for you. Learn more. > http://windows.microsoft.com/shop > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091203/31581af5/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 3 Dec 2009 11:23:46 +0200 > From: Ozge Engin <ozge.en...@gmail.com> > Subject: [gmx-users] "coarse_grain.tcl" script does not show all of > the coarse-grained bonds in vmd > To: gmx-users@gromacs.org > Message-ID: > <373874cf0912030123q30e9dd86ve61c8845eec46...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I was trying to show the bonds between my CG beads in VMD. I have four CG > beads per each molecule, and there are 18 separate molecules which contain > these four beads, which results in having 72 CG beads in total. Therefore, > I expect to see 54 CG bonds in the end. > > I used the "coarse_grain.tcl" script to visualize these CG bonds as > suggested on the VMD page. I have two different bead types in the system: > CA > and CG. In order to visualize the bonds I used the following command line > on > Tk console: > > source coarse_grained.tcl > g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice} > -color {name name} > > After that it gave me the following lines: > > [ g_cg ] Processing "topol.tpr"... > [ g_cg ] Create the bond list for 72 atoms... > [ g_cg ] Rebuild bonds... > [ g_cg ] Create representations... > > which I understood that all the bonds are created successfully, but when I > looked at the screen I could see only one of those CG bonds, but not the > others. Why might be the reason? > > Thanks in advance > -- > Ozge Engin > ★☆ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091203/78093f12/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 03 Dec 2009 10:54:28 +0100 > From: Nicolas Sapay <nicolas.sa...@cermav.cnrs.fr> > Subject: Re: [gmx-users] "coarse_grain.tcl" script does not show all > of the coarse-grained bonds in vmd > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4b178ad4.7000...@cermav.cnrs.fr> > Content-Type: text/plain; charset="utf-8" > > > > Ozge Engin a écrit : > > Hi all, > > > > I was trying to show the bonds between my CG beads in VMD. I have four > > CG beads per each molecule, and there are 18 separate molecules which > > contain these four beads, which results in having 72 CG beads in > > total. Therefore, I expect to see 54 CG bonds in the end. > > > > I used the "coarse_grain.tcl" script to visualize these CG bonds as > > suggested on the VMD page. I have two different bead types in the > > system: CA and CG. In order to visualize the bonds I used the > > following command line on Tk console: > > > > source coarse_grained.tcl > > g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice > > Licorice} -color {name name} > Hi, > > you mentionned that you have 2 types of beads called CA and CG. Here, > you are selecting beads named CA and CB. Maybe that's where the problem > come from. Try to modify the representations manually (from the > "representation" menu) to see if it change something. If not, that is > probably a bug in the parsing of the gmxdump output. That is where the > bonds come from. > > Cheers, > Nicolas > > > > After that it gave me the following lines: > > > > [ g_cg ] Processing "topol.tpr"... > > [ g_cg ] Create the bond list for 72 atoms... > > [ g_cg ] Rebuild bonds... > > [ g_cg ] Create representations... > > > > which I understood that all the bonds are created successfully, but > > when I looked at the screen I could see only one of those CG bonds, > > but not the others. Why might be the reason? > > > > Thanks in advance > > -- > > Ozge Engin > > ★☆ > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: nicolas_sapay.vcf > Type: text/x-vcard > Size: 403 bytes > Desc: not available > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091203/b71300bf/nicolas_sapay.vcf > > ------------------------------ > > -- > 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/search before posting! > > End of gmx-users Digest, Vol 68, Issue 21 > ***************************************** > -- Ozge Engin ★☆
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