[gmx-users] problem in simulation of dna-protein complex
Dear all I am doing simulation of DNA -protein complex using amber port with gromacs-4.0.3 . for this I have to make changes in my .pdb file a/c to entry in .rtp file of amber force field. I have all possible changes but when I run the pdb2gmx command the error came like this- Fatal error: Atom O2 in residue DT 1 not found in rtp entry with 32 atoms while sorting atoms and entry of atom in .rtp file like this- Pamber99_461.16590 1 O1Pamber99_45 -0.77610 2 O2Pamber99_45 -0.77610 3 O5'amber99_44 -0.49540 4 C5'amber99_11 -0.00690 5 H5'1amber99_190.07540 6 H5'2amber99_190.07540 7 C4'amber99_110.16290 8 H4'amber99_190.11760 9 O4'amber99_44 -0.3691010 C1'amber99_110.0680011 H1'amber99_200.1804012 N1amber99_40 -0.0239013 C6amber99_7-0.2209014 H6amber99_230.2607015 C5amber99_7 0.0025016 C7amber99_11 -0.2269017 H71amber99_180.0770018 H72amber99_180.0770019 H73amber99_180.0770020 C4amber99_2 0.5194021 O4amber99_41 -0.5563022 N3amber99_35 -0.4340023 H3amber99_170.3420024 C2amber99_2 0.5677025 Oamber99_41 -0.5881026 C3'amber99_110.0713027 H3'amber99_190.0985028 C2'amber99_11 -0.0854029 H2'1amber99_180.0718030 H2'2amber99_180.0718031 O3'amber99_44 -0.5232032 So, can anyone suggest me at the place 02 what name I can change in my .pdb file. Thanking you Nitu sharma ___ gmx-users mailing listgmx-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
Re: [gmx-users] How to avoid generating wrong dihedrals?
Hi Chaofu Wu, Indeed it seems improper to have a dihedral with C-N-H-H. So it's an improper dihedral! :p The problem might arise from the addition of hydrogens. Could you give more information? Which force field did you use? what residue was causing the problem? Can you reproduce the problem starting only with that residue (and then paste it, so that one of us might reproduce it)? Cheers, Tsjerk 2009/7/1 wuxiao xiaowu...@hotmail.com: Dear gmx users, I try to generate gro and top files using pdb2gmx, and this procedure finishs without any error. However, when I run grompp from these files, many errors are encountered such as: .. ERROR 124 [file g04.top, line 20027] No default Ryckaert-Bell. types .. I gusess it is dihedrals that cause these errors. So I look for the line 20027 in the file g04.top. only to find that these dihedrals are C-N-H-H, obviously wrong. How to avoid these errors? Could you give me some help to cope with them? Thank you for attention. Sincerely, Chaofu Wu 把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！ ___ gmx-users mailing listgmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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
Re: [gmx-users] problem in simulation of dna-protein complex
Hi Nitu, Check the atoms and their order in the pdb and the rtp file and try to find out which match and which miss. C2 amber99_2 0.56770 25 O amber99_41 -0.58810 26 I place my bet on this one. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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
[gmx-users] GMX Installation
Dear GMX Users, I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet. Please guide me if you have information on this case. Thanks. Mahmoud ___ gmx-users mailing listgmx-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
Re: [gmx-users] GMX Installation
mahmoud wrote: Dear GMX Users, I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet. Please guide me if you have information on this case. You should search the web for information on installing RPMs, or follow the instructions on the GROMACS webpage for installation from the source tarball here - http://oldwww.gromacs.org/content/view/19/32/ Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] GMX Installation
Dear GMX Users, I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet. If you want some help from the mailing list, you have to be a bit more specific about your problem. You can also read the documentation available here: http://oldwww.gromacs.org/content/view/23/33/ http://oldwiki.gromacs.org/index.php/Installation Nicolas Please guide me if you have information on this case. Thanks. Mahmoud ___ gmx-users mailing listgmx-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 -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44 ___ gmx-users mailing listgmx-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
Re: [gmx-users] Table Functions
Devin Averett wrote: Hi- I am trying to add an extra repulsive potential for neighboring hydroxyl groups on a carbon chain and have heard that this can be done using table functions. Is there a good resource on how to create these table function files or even someplace where I could get an example of them? That's upside-down. You can add an extra potential in the topology. If you need a functional form you might choose to add a table potential. Either way, you'll need to know chapter 5 in the manual, and some other sections for table potentials. Mark ___ gmx-users mailing listgmx-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
Re: [gmx-users] Installation problem:fftw3f lib. not found.
* Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-30 21:19:47 -0400]: Hi, I installed fftw as follows (creating single- and double-precision versions) : ./configure --enable-threads --enable-float --prefix=/home/kudesias/fftw make make install make distclean ./configure --enable-threads --prefix=/home/kudesias/fftw make make install I also used export CPPFLAGS=-I/home/kudesias/fftw/include export LDFLAGS=-L/home/kudesias/fftw/lib ( Initially I used I in place of L so I corrected it) On using the configure script ./configure --enable-mpi I get the following error then checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... configure: error: Cannot find the default external FFT library (fftw3). I will be glad if you can help with this. I tried your procedure on my computer and the configure script finished without trouble. Are your sure using fftw**3** ? In case you use fftw2 you have to tell the script. Another problem can be that you set the enviroment variables in another shell window as you execute the configure script, because then CPPFLAGS and LDFLAGS are not present anymore. To be on the safe side put all in one line: ./configure --prefix=$HOME/gmx4 LDFLAGS=-L$HOME/fftw/lib CPPFLAGS=-I$HOME/fftw/include This command line should work for you, in case FFTW3 is located as you mentioned before. So try copypaste and tell us over the mailing list what happend. Flo Thanks On Thu, Jun 25, 2009 at 2:08 AM, Florian Dommert domm...@icp.uni-stuttgart.de wrote: * Shobhit Kudesia shobhit.kude...@gmail.com [2009-06-25 01:55:00 +0530]: Hi , During the ./configure of gromacs on my Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3 files in a directory other than usr/local. I have installed fftw3 both with double and single precision but I still get the error while configuration of GROMACS for default single precision. I have also included the libraries usinG CPPFLAGS LDFLAGS. If you have installed the single version of FFTW3 and supply the corresponding CPPFLAGS and LDFLAGS to configure then the script will find the libraries. So two errors are very likely though we do not anything about your installation: * a small typo in the configure line ( if you present it here, everybody can judge this ) * the installation of the single precision fftw3f failed for any reasons Flo Any help will be appreciated ___ gmx-users mailing listgmx-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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommerthttp://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert !! PGP-ENCODED emails preferred !! ___ gmx-users mailing listgmx-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 -- With Warm Regards Shobhit Kudesia 3rd year Undergraduate Department of Biotechnology IIT Kharagpur ___ gmx-users mailing listgmx-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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !! pgpGSE3bxSKTA.pgp Description: PGP signature ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!
Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)
Dear Tsjerk and other gmx users and developers, I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively. The both repeating units cause the problem. When I delete all those wrong dihedrals in the top file, the grompp and mdrun can run successfully. I check the top file. It seems that other dihedrals are all correct. What to happen to this? Could you give me further information? Any reply would be thanked very much. Sincerely, Chaofu Wu Hi Chaofu Wu, Indeed it seems improper to have a dihedral with C-N-H-H. So it's an improper dihedral! :p The problem might arise from the addition of hydrogens. Could you give more information? Which force field did you use? what residue was causing the problem? Can you reproduce the problem starting only with that residue (and then paste it, so that one of us might reproduce it)? Cheers, Tsjerk _ 打工，挣钱，买房子，快来MClub一起”金屋藏娇”！ http://club.msn.cn/?from=10___ gmx-users mailing listgmx-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
Re: [gmx-users] How to avoid generating wrong dihedrals?(Tsjerk)
wuxiao wrote: Dear Tsjerk and other gmx users and developers, I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of hydrogens is found correct. The rtp files were written for the core, middle and end repeating units, respectively. The both repeating units cause the problem. When I delete all those wrong dihedrals in the top file, the grompp and mdrun can run successfully. I check the top file. It seems that other dihedrals are all correct. What to happen to this? Could you give me further information? Any reply would be thanked very much. I think it likely you have a malformed [ dihedrals ] section in your .rtp file. pdb2gmx will generate dihedrals for each rotatable bond (see manual section 5.6.1), so the only way you can get such a dihedral is to have defined all three of those bonds, or specifically defined that dihedral. Perhaps these bonds are being created erroneously by your .hdb? You will have to look in detail at what you are doing with these. Mark ___ gmx-users mailing listgmx-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
[gmx-users] Energy analysis by mdrun -rerun
hi,gmx-users I run a simulation with mdrun -rerun like this: mdrun -s rerun.tpr -rerun md.trr -o rerun.trr -e rerun.edr -g rerun.log Then I run g_energy -f rerun.edr -o LJ-SR.xvg I observed a strange behavior that the avarge value of LJ-SR in the screen is very different from the value in the LJ-SR.xvg. I would like to know how to produce the difference and which values are correct. 1.The value in the screen : Last frame read 1 time 2000.000 Statistics over 101 steps [ 0. thru 2000.0001 ps ], 1 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- LJ (SR) -10.8964243.195 242.098 0.0399779.9401 gcq#37: They Were So Quiet About It (Pixies) 2.The value in the LJ-SR.xvg: 1976.000122 -5333.091309 1977.000122 -5498.676758 1978.000122 -5322.309570 1979.000122 -5375.214355 1980.000122 -5580.856934 1981.000122 -5407.598633 1982.000122 -5369.188477 1983.000122 -5584.138672 1984.000122 -5534.824707 1985.000122 -5361.794922 1986.000122 -5374.747070 1987.000122 -5531.766602 1988.000122 -5464.309082 1989.000122 -5391.916504 1990.000122 -5294.478516 1991.000122 -5369.667969 1992.000122 -5499.476562 1993.000122 -5444.689941 1994.000122 -5333.860352 1995.000122 -5436.152344 1996.000122 -5352.176758 1997.000122 -5397.282227 1998.000122 -5356.059570 1999.000122 -5333.074707 2000.000122 -5425.871582 Jinyao Wang wan...@ciac.jl.cn 2009-07-01 ___ gmx-users mailing listgmx-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
[gmx-users] Problem with AMBER-GROMACS DNA database residue
Hi, gmx-users, I have a problem to translate nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT-- DTHY, DG--DGUA, DC--DCYT, DA--DADE, in order to translate the MDs from AMBER to GROMACS... but in the prmtop file are present also DT5, CT3, that indicate the residues at the end of the chains... anyone knows which is the correct GROMACS residue name for these residues? I have searched in the ff.rtp file but seem that these particular residues are not present... Thank you in advance... ___ gmx-users mailing listgmx-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
[gmx-users] Re: Problem with AMBER-GROMACS DNA database residue
Hi there, Not really clear what you did or want to do, so I'll do assumptions. If your have you prmtop and inpcrd files working fine with AMBER (sand or pmemd) then you just want to run this with GMX (mdrun ...). So, you can try amb2gmx.pl program or (better), look at acpypi.googlecode.com, and you can find how to use 'acpypi' for converting amber topology files to gromacs topol files. Cheers, Alan On Wed, Jul 1, 2009 at 10:25, gmx-users-requ...@gromacs.org wrote: Hi, gmx-users, I have a problem to translate nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT-- DTHY, DG--DGUA, DC--DCYT, DA--DADE, in order to translate the MDs from AMBER to GROMACS... but in the prmtop file are present also DT5, CT3, that indicate the residues at the end of the chains... anyone knows which is the correct GROMACS residue name for these residues? I have searched in the ff.rtp file but seem that these particular residues are not present... Thank you in advance... -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-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
[gmx-users] make index group
Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. I did not make index before I proceed with grompp for the mdrun, is it cause by this? thanks. Regards, bing ___ gmx-users mailing listgmx-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
Re: [gmx-users] Re: Problem with AMBER-GROMACS DNA database residue
Hi, Alan Thank you very much for your quick answer. You understand well my problem... I normally use amb2gmx for proteins, and, changing some residue names (ex. CYM--CYS..), it works correctly... It's the first time that I work with DNA, and I have this problem... thank you for your help Rubben 2009/7/1 Alan alanwil...@gmail.com Hi there, Not really clear what you did or want to do, so I'll do assumptions. If your have you prmtop and inpcrd files working fine with AMBER (sand or pmemd) then you just want to run this with GMX (mdrun ...). So, you can try amb2gmx.pl program or (better), look at acpypi.googlecode.com, and you can find how to use 'acpypi' for converting amber topology files to gromacs topol files. Cheers, Alan On Wed, Jul 1, 2009 at 10:25, gmx-users-requ...@gromacs.org wrote: Hi, gmx-users, I have a problem to translate nitrogen base residue names from AMBER to GROMACS. I have simulated with AMBER a DNA-protein complex, then i have changed in the prmtop file the standard nitrogen bases as DT-- DTHY, DG--DGUA, DC--DCYT, DA--DADE, in order to translate the MDs from AMBER to GROMACS... but in the prmtop file are present also DT5, CT3, that indicate the residues at the end of the chains... anyone knows which is the correct GROMACS residue name for these residues? I have searched in the ff.rtp file but seem that these particular residues are not present... Thank you in advance... -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 ___ gmx-users mailing listgmx-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 ___ gmx-users mailing listgmx-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
[gmx-users] norm of force = nan error
dear justin, i recently got this error: Norm of force = nan (not a number) while doing a 5000 step energy minimization. the em gets over in just 1 step and this error is shown.how do i rectify this? thank you. Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-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
Re: [gmx-users] GMX Installation
On Wed, 2009-07-01 at 01:01 -0700, mahmoud wrote: Dear GMX Users, I want to Install Gromacs on Fedora 10 x86_64. I downloaded the rpm files of FFTW and Gromacs, however, I can not install the gromacs yet. Please guide me if you have information on this case. You can just install the Fedora version by # yum -y install gromacs If you need MPI support, do # yum -y install gromacs-mpi If you don't want gromacs to be updated [automatically], just put the line exclude=gromacs into /etc/yum.conf If you want to compile gromacs yourself, just # yum -y install fftw-devel openmpi-devel gsl-devel lapack-devel and proceed with the Gromacs compilation. -- -- 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 -- ___ gmx-users mailing listgmx-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
Re: [gmx-users] make index group
Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation recipe from some tutorial, go back to that and understand what this step is designed to achieve, and then adjust it to suit your new context. Mark ___ gmx-users mailing listgmx-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
[gmx-users] problem during simulation of dna-protein complex
Dear Tsjerk Thanks for your right suggestion. It works successfully for dna-protein complex simulation. i want to ask one more thing , can I use parameter file for energy minimisation which i have used for membrane protein simulation or can u suggest me what changes I have to make in parameter file to use for dna- protein complex simulation. the parameter file like this- cpp = /usr/bin/cpp define = -DPOSRE_PROTEIN constraints = none integrator = steep dt = 0.002 nsteps = 1 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.0001 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Specially where i have apply position restrain? Thanking you Nitu sharma ___ gmx-users mailing listgmx-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
Re: [gmx-users] make index group
Mark Abraham wrote: Bing Bing wrote: Dear all, I'm trying to perform order parameter analysis. I 've use :- make_ndx_d -f xxx.tpr -o sn1.ndx 15 a Cxx |... q i've got this error :- Group 15 not exist. So use a group that does exist. If you're copying an index group creation recipe from some tutorial, go back to that and understand what this step is designed to achieve, and then adjust it to suit your new context. In addition to Mark's advice, please see the wiki page for g_order; it explains exactly how to create the necessary index groups. If you're merging groups on into one, as it appears you are, you're doing it wrong. http://oldwiki.gromacs.org/index.php/g_order -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
Re: [gmx-users] norm of force = nan error
P.R.Anand Narayanan wrote: dear justin, i recently got this error: Norm of force =nan (not a number) while doing a 5000 step energy minimization. the em gets over in just 1 step and this error is shown.how do i rectify this? You either have severe atomic overlap or an otherwise broken structure, such that energy minimization fails immediately. -Justin thank you. Love Cricket? Check out live scores, photos, video highlights and more. Click here http://in.rd.yahoo.com/tagline_cricket_2/*http://cricket.yahoo.com. ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
[gmx-users] Rigid body-LINCS warning
Dear Gromacs users,I try to run a molecular dynamics simulation of a polyoxometalate. I want the molecule to behave as a rigid body except for one peptidic chain bound to it. To achieve this, I constrain all the relative distances between every possible couple of atoms in the structure. I add the constraints to my topology file (*.top). After creating the *.tpr file, the problem is that mdrun gives several LINCS WARNINGS and finally crashes.I do not know what I am doing wrong as every constraint is correct when used independently.I would be very grateful if anyone could give me a clue as to what causes the problem.Thank youEva___ gmx-users mailing listgmx-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
[gmx-users] umbrella sampling: pdo file not generated
Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log $mol.out I think everything is OK (it's working on GROMACS 3.3), but the pdo file has NOT been generated. How can I generate it from tpr, trr ou xct output files? Is there another option to get the pdo file? Thanks a lot, Gustavo -- Dr. Gustavo Velardez Kemisk Institut Danmarks Tekniske Universitet (DTU) Danmark ___ gmx-users mailing listgmx-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
Re: [gmx-users] umbrella sampling: pdo file not generated
Justin A. Lemkul skrev: Gustavo Velardez wrote: Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log $mol.out I think everything is OK (it's working on GROMACS 3.3), but the pdo file has NOT been generated. How can I generate it from tpr, trr ou xct output files? Is there another option to get the pdo file? The pull code has changed substantially between version 3.3.x and 4.0.x; upgrade to 4.0.5 (to take advantage of several bug fixes), read the documentation and revision history, and try again. -Justin Indeed. Some of those flags have completely different meaning now, and others don't exist anymore. That should be obvious from mdrun -h. /Erik Thanks a lot, Gustavo -- Dr. Gustavo Velardez Kemisk Institut Danmarks Tekniske Universitet (DTU) Danmark ___ 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 -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-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
Re: [gmx-users] umbrella sampling: pdo file not generated
Gustavo Velardez wrote: Hi all, I ran a calculation using GROMACS 4.0.3 and this command line: mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po pullout.ppa -pn index5000.ndx -g $mol.log $mol.out I think everything is OK (it's working on GROMACS 3.3), but the pdo file has NOT been generated. How can I generate it from tpr, trr ou xct output files? Is there another option to get the pdo file? The pull code has changed substantially between version 3.3.x and 4.0.x; upgrade to 4.0.5 (to take advantage of several bug fixes), read the documentation and revision history, and try again. -Justin Thanks a lot, Gustavo -- Dr. Gustavo Velardez Kemisk Institut Danmarks Tekniske Universitet (DTU) Danmark ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
Re: [gmx-users] disable ulimit
Thanks Ansgar
We'll try it.
Dr Gustavo Fioravanti Vieira
Núcleo de Bioinformática do Laboratório de Imunogenética
Bolsista PNPD do Programa de Pós-Graduação em Genética e Biologia Molecular
UFRGS
--- Em seg, 29/6/09, Ansgar Esztermann aesz...@gwdg.de escreveu:
De: Ansgar Esztermann aesz...@gwdg.de
Assunto: Re: [gmx-users] disable ulimit
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Data: Segunda-feira, 29 de Junho de 2009, 12:58
Hi Gustavo,
On Jun 24, 2009, at 20:48 , Gustavo Fioravanti wrote:
we are trying to run mdrun_mpi in a public cluster of our university.
However, we got the following error:
/etc/profile.d/limits.sh: line 1: ulimit: max locked memory: cannot modify
limit: Operation not permitted
There are two kinds of ulimits, soft and hard. Hard limits cannot be increased,
so maybe you try to exceed a hard limit here?
/var/tmp/sge_local_spool/r01n19/job_scripts/3051: line 10: grompp_mpi:
command not found
The cluster has already settled to unlimited access to memory. However,
grompp hasn't have permission to modify this file (limits.sh).
I do not think grompp tries to modify the file. The error message above seems
to point at limits.sh not being allowed to raise the limit. Did you talk to
your sysadmin? They should be able to raise the limit. BTW, note that the limit
in question here is not memory per se, but locked memory.
I would like to disable the ulimit function at source file from GROMACS. How
can I do that?
Try to do it from a script (or by hand) before starting gromacs, like so:
ulimit -l unlimited
Modifying the limit from the program is also possible, but a little bit more
involved (this code should work on Linux; on other systems, things might be a
bit different):
#include sys/resource.h
struct rlimit unlim = {RLIM_INFINITY, RLIM_INFINITY};
int err = setrlimit(RLIMIT_MEMLOCK, unlim);
/* error handling skeleton; based on the error message given above, you will
probably get EPERM */
if (err)
switch (errno)
{
case EFAULT: /* limit points outside address range */
break;
case EINVAL: /* invalid resource, or soft hard */
break;
case EPERM: /* unprivileged process tried to raise hard limit */
break;
}
A.
--Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
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[gmx-users] How to set fourierspacing?
Dear colleagues, I use PME to consider coulomb interactions. It seems that the fourierspacing is an important parameter. When it is set a larger value, the calculation can be much faster. But what is the disadvantages of using a larger value? I wish to get you help. Best Regards, Chaofu Wu _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ gmx-users mailing listgmx-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
Re: [gmx-users] How to set fourierspacing?
wuxiao wrote: Dear colleagues, I use PME to consider coulomb interactions. It seems that the fourierspacing is an important parameter. When it is set a larger value, the calculation can be much faster. But what is the disadvantages of using a larger value? I wish to get you help. Faster, yes, but also less accurate. There's a complex interaction of * your hardware, * your FFT library, * the GROMACS kernel performance, * rcoulomb, * ewald_rtol, * fourierspacing, * pme_order and * (in parallel) your number of PME nodes that determines the accuracy and speed of the PME approximation to the full electrostatic interactions. Carsten Kutzner has previously posted to this list some heuristics for varying fourierspacing. Search for them. Mark ___ gmx-users mailing listgmx-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
[gmx-users] GMX-Installation2
Dear Jussi, Hi, Thanks for your help, Because of some problems with fedora 10, I installed Fedora 11. Unfortunately, I can not understand the instructions of your e-mail. I am new with Gromacs! Now, all of required files of gromacs 4 are completely installed on computer, however, it can not be RUN ! Would you please let me know again the required information! Thanks again, Best, Mahmoud ___ gmx-users mailing listgmx-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
Re: [gmx-users] problem during simulation of dna-protein complex
Hi Nitu, Energy minimization is only to remove some strain from your system. You probably don't want to include position restraints there. After energy minimization you typically run a short MD run in which you use position restraints such that the protein/DNA doesn't move to much, but the water can equilibrrate with respect to the protein. Check the tutorial material linked on the wiki. This stuff is mentioned in all of them. Cheers, Tsjerk On Wed, Jul 1, 2009 at 2:06 PM, nitu sharmasharmanit...@gmail.com wrote: Dear Tsjerk Thanks for your right suggestion. It works successfully for dna-protein complex simulation. i want to ask one more thing , can I use parameter file for energy minimisation which i have used for membrane protein simulation or can u suggest me what changes I have to make in parameter file to use for dna- protein complex simulation. the parameter file like this- cpp = /usr/bin/cpp define = -DPOSRE_PROTEIN constraints = none integrator = steep dt = 0.002 nsteps = 1 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.0001 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Specially where i have apply position restrain? Thanking you Nitu sharma ___ gmx-users mailing list gmx-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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
Re: [gmx-users] GMX-Installation2
nanogr...@ymail.com wrote: Dear Jussi, Hi, Thanks for your help, Because of some problems with fedora 10, I installed Fedora 11. Unfortunately, I can not understand the instructions of your e-mail. I am new with Gromacs! That won't get you any more help. We're all busy people, and we're not going to spend time guessing exactly what your problem is. You need to provide as much diagnostic information as you think you have. That means what commands you tried, what you expected to happen, and what actually happened. Now, all of required files of gromacs 4 are completely installed on computer, however, it can not be RUN ! Would you please let me know again the required information! Maybe http://oldwiki.gromacs.org/index.php/Installation will help. Mark ___ gmx-users mailing listgmx-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
