[gmx-users] gromacs installation error
Hi Gromacs users, Am trying to install gromacs-4.5.5 version on IBM cluster with Linux platform and am getting an error such as configure: error: Cannot find fftw3f library. The steps i followed- Installed fftw-3.3 version ./configure --enable-threads --enable-float make make install setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- gmx-users mailing listgmx-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
[gmx-users] problem installing gromacs
Hi everyone, I have installed Gromacs 4.5.5 following the online installation guide without and with mpi. My configure lines (after few tries) were: ./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++ --prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3 --disable-shared --without-pic --program-suffix=_d ./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++ --prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3 --disable-shared --without-pic --program-suffix=_d_mpi --enable-mpi The binary files were created for both configurations but I get error messages in the config.log files (see below) and I was wondering if these errors are critical. error messages for the installation without mpi: conftest.c:20:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:20:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:40:13: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' conftest.c:54:4: error: 'not' undeclared (first use in this function) conftest.c:54:8: error: expected ';' before 'big' conftest.cpp:43:28: fatal error: ac_nonexistent.h: No such file or directory conftest.cpp:43:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:86:20: fatal error: direct.h: No such file or directory conftest.c:53:20: fatal error: direct.h: No such file or directory conftest.c:71:1: error: void value not ignored as it ought to be conftest.c:102:20: error: expected expression before ')' token conftest.c:110:13: error: 'bool' undeclared (first use in this function) conftest.c:119:21: error: expected expression before ')' token conftest.c:89:20: error: expected expression before ')' token conftest.c:90:20: error: expected expression before ')' token conftest.c:91:27: error: expected expression before ')' token error messages for the installation with mpi: conftest.c:24:2: error: #error not catamount | #error not catamount conftest.c:23:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:23:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:24:13: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' conftest.c:38:4: error: 'not' undeclared (first use in this function) conftest.c:38:8: error: expected ';' before 'big' /private/gnss/local/bin/gcc: error trying to exec '/private/gnss/local/bin/x86_64-unknown-linux-gnu-gcc--I/opt/intel/impi/3.2.2.006/include64http://3.2.2.006/include64': execvp: No such file or directory conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:70:20: fatal error: direct.h: No such file or directory conftest.c:37:20: fatal error: direct.h: No such file or directory conftest.c:55:1: error: void value not ignored as it ought to be conftest.c:86:20: error: expected expression before ')' token conftest.c:94:13: error: 'bool' undeclared (first use in this function) conftest.c:103:21: error: expected expression before ')' token conftest.c:73:20: error: expected expression before ')' token conftest.c:74:20: error: expected expression before ')' token conftest.c:75:27: error: expected expression before ')' token I saw some of these errors in gromacs mailing list but couldn't understand if these errors were eventually solved and how. Thanks, Efrat -- gmx-users mailing listgmx-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
[gmx-users] RE: logfile size
Dear All, Hope this is not tooo stupid a question. I recenttly reduced my file sizes by increasing the time between writing. However, if I do an Umbrella run I get the following to my logfile output, which makes my log file in the end larger than my trajectory; Dispersion correction V -5.49759e+03 dVdl 0.0e+00 Dispersion correction V -5.49756e+03 dVdl 0.0e+00 Dispersion correction V -5.49753e+03 dVdl 0.0e+00 Dispersion correction V -5.49750e+03 dVdl 0.0e+00 Dispersion correction V -5.49747e+03 dVdl 0.0e+00 Dispersion correction V -5.49744e+03 dVdl 0.0e+00 Dispersion correction V -5.49741e+03 dVdl 0.0e+00 Dispersion correction V -5.49738e+03 dVdl 0.0e+00 Dispersion correction V -5.49735e+03 dVdl 0.0e+00... Does anyone know how to turn this off for the logfile, I get one of these for each step, instead of for each write step? My write portion of the .mdp file is; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.0002 ; 2 fs tinit = 0 ; Output control nstxout = 10 ; save coordinates every 0.2 ps nstvout = 10 ; save velocities every 0.2 ps nstenergy = 10 ; save energies every 0.2 ps nstcalcenergy = 100 nstfout = 10 nstlog = 10 ; update log file every 0.2 ps nstxtcout = 10 Any quick help is appriciated. Sincerely, Stephan Lloyd Watkins -- NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-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
Re: [gmx-users] gromacs installation error
Are you sure that fftw was installed in /home/fftw? According to the instructions you used to install fftw, it seems that it's been done in the standard location (maybe /usr/local/fftw?), anyway in such a case the system should normally find the libraries without additional CPPFLAGS and LDFLAGS. If not in /home/fftw, try to find where the libraries were installed and change CPPFLAGS and LDFLAGS accordingly (or restart a new session and try without setenv calls) Javier El 06/12/11 10:10, aiswarya pawar escribió: Hi Gromacs users, Am trying to install gromacs-4.5.5 version on IBM cluster with Linux platform and am getting an error such as configure: error: Cannot find fftw3f library. The steps i followed- Installed fftw-3.3 version ./configure --enable-threads --enable-float make make install setenv CPPFLAGS -I/home/fftw/include setenv LDFLAGS -L/home/fftw/lib In gromacs-4.5.5 directory ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3 in this i got the error. please help. Thanks, Aiswarya -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-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
Re: [gmx-users] RE: logfile size
On 6/12/2011 8:48 PM, lloyd riggs wrote: Dear All, Hope this is not tooo stupid a question. I recenttly reduced my file sizes by increasing the time between writing. However, if I do an Umbrella run I get the following to my logfile output, which makes my log file in the end larger than my trajectory; Dispersion correction V -5.49759e+03 dVdl 0.0e+00 Dispersion correction V -5.49756e+03 dVdl 0.0e+00 Dispersion correction V -5.49753e+03 dVdl 0.0e+00 Dispersion correction V -5.49750e+03 dVdl 0.0e+00 Dispersion correction V -5.49747e+03 dVdl 0.0e+00 Dispersion correction V -5.49744e+03 dVdl 0.0e+00 Dispersion correction V -5.49741e+03 dVdl 0.0e+00 Dispersion correction V -5.49738e+03 dVdl 0.0e+00 Dispersion correction V -5.49735e+03 dVdl 0.0e+00... Does anyone know how to turn this off for the logfile, I get one of these for each step, instead of for each write step? My write portion of the .mdp file is; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.0002 ; 2 fs tinit = 0 ; Output control nstxout = 10 ; save coordinates every 0.2 ps nstvout = 10 ; save velocities every 0.2 ps nstenergy = 10 ; save energies every 0.2 ps nstcalcenergy = 100 nstfout = 10 nstlog = 10 ; update log file every 0.2 ps nstxtcout = 10 Check out the list of options in mdrun -h. There's one that will completely stop this printing. I think it's supposed to print this stuff only according to nstlog, but the code is slightly broken here. I'll suggest a fix. 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/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
Re: [gmx-users] RE: logfile size
On 7/12/2011 12:12 AM, Mark Abraham wrote: On 6/12/2011 8:48 PM, lloyd riggs wrote: Dear All, Hope this is not tooo stupid a question. I recenttly reduced my file sizes by increasing the time between writing. However, if I do an Umbrella run I get the following to my logfile output, which makes my log file in the end larger than my trajectory; Dispersion correction V -5.49759e+03 dVdl 0.0e+00 Dispersion correction V -5.49756e+03 dVdl 0.0e+00 Dispersion correction V -5.49753e+03 dVdl 0.0e+00 Dispersion correction V -5.49750e+03 dVdl 0.0e+00 Dispersion correction V -5.49747e+03 dVdl 0.0e+00 Dispersion correction V -5.49744e+03 dVdl 0.0e+00 Dispersion correction V -5.49741e+03 dVdl 0.0e+00 Dispersion correction V -5.49738e+03 dVdl 0.0e+00 Dispersion correction V -5.49735e+03 dVdl 0.0e+00... Does anyone know how to turn this off for the logfile, I get one of these for each step, instead of for each write step? My write portion of the .mdp file is; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.0002 ; 2 fs tinit = 0 ; Output control nstxout = 10 ; save coordinates every 0.2 ps nstvout = 10 ; save velocities every 0.2 ps nstenergy = 10 ; save energies every 0.2 ps nstcalcenergy = 100 nstfout = 10 nstlog = 10 ; update log file every 0.2 ps nstxtcout = 10 Check out the list of options in mdrun -h. There's one that will completely stop this printing. I think it's supposed to print this stuff only according to nstlog, but the code is slightly broken here. I'll suggest a fix. Nah, the code looks fine - it should only ever print at nstlog steps. 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/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
Re: [gmx-users] problem installing gromacs
On 6/12/2011 9:09 PM, Efrat Exlrod wrote: Hi everyone, I have installed Gromacs 4.5.5 following the online installation guide without and with mpi. My configure lines (after few tries) were: ./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++ --prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3 --disable-shared --without-pic --program-suffix=_d ./configure CC=/private/gnss/local/bin/gcc CXX=/private/gnss/local/bin/g++ --prefix=/private/gnss/Gromacs_455 --disable-float --with-fft=fftw3 --disable-shared --without-pic --program-suffix=_d_mpi --enable-mpi The binary files were created for both configurations but I get error messages in the config.log files (see below) and I was wondering if these errors are critical. error messages for the installation without mpi: conftest.c:20:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:20:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:40:13: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' conftest.c:54:4: error: 'not' undeclared (first use in this function) conftest.c:54:8: error: expected ';' before 'big' conftest.cpp:43:28: fatal error: ac_nonexistent.h: No such file or directory conftest.cpp:43:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:86:20: fatal error: direct.h: No such file or directory conftest.c:53:20: fatal error: direct.h: No such file or directory conftest.c:71:1: error: void value not ignored as it ought to be conftest.c:102:20: error: expected expression before ')' token conftest.c:110:13: error: 'bool' undeclared (first use in this function) conftest.c:119:21: error: expected expression before ')' token conftest.c:89:20: error: expected expression before ')' token conftest.c:90:20: error: expected expression before ')' token conftest.c:91:27: error: expected expression before ')' token error messages for the installation with mpi: conftest.c:24:2: error: #error not catamount | #error not catamount conftest.c:23:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:23:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:24:13: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a' conftest.c:38:4: error: 'not' undeclared (first use in this function) conftest.c:38:8: error: expected ';' before 'big' /private/gnss/local/bin/gcc: error trying to exec '/private/gnss/local/bin/x86_64-unknown-linux-gnu-gcc--I/opt/intel/impi/3.2.2.006/include64 http://3.2.2.006/include64': execvp: No such file or directory conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory conftest.cpp:27:28: fatal error: ac_nonexistent.h: No such file or directory conftest.c:70:20: fatal error: direct.h: No such file or directory conftest.c:37:20: fatal error: direct.h: No such file or directory conftest.c:55:1: error: void value not ignored as it ought to be conftest.c:86:20: error: expected expression before ')' token conftest.c:94:13: error: 'bool' undeclared (first use in this function) conftest.c:103:21: error: expected expression before ')' token conftest.c:73:20: error: expected expression before ')' token conftest.c:74:20: error: expected expression before ')' token conftest.c:75:27: error: expected expression before ')' token I saw some of these errors in gromacs mailing list but couldn't understand if these errors were eventually solved and how. configure runs a bunch of tests to see what properties your system has. Some of these tests will fail. This is not a problem if configure, make and GROMACS later succeed. 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/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
Re: [gmx-users] RMDS calculation
Sorry but the help does not help me... In anycase, the help of g_rmsdist say: g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by g_rms...; so no fit is needed, for me it means that there is no superimposition... Can you explain me where I'm wrong? Valerio Tsjerk Wassenaar tsje...@gmail.com ha scritto: Hi Valerio, Check the help for both tools. That explains it all. Oh, and you're not correct ;) Cheers, Tsjerk On Mon, Dec 5, 2011 at 4:42 PM, vferra...@units.it wrote: Dear all, I need to calculate the RMSD of a protein during time. So that I've calculated the trajectory; for the calculation which tool should I use? g_rms or g_rmsdist ? Which is the difference between these two tools? If I'm right the main difference is that with g_rms the structure at the time t is superimposed to the reference structure before calculate the RMSD, while with g_rmsdist the RMSD is calculated without any superimposition, am I correct? Valerio This message was sent using IMP, the Internet Messaging Program. -- 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-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 This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-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
[gmx-users] mmView - a tool for mmCIF exploration
Dear colleagues, We would like to announce the availability of mmView - the web-based application which allows to comfortably explore the structural data of biomacromolecules stored in the mmCIF (macromolecular Crystallographic Information File) format. The mmView software system is primarily intended for educational purposes but it can also serve as an auxiliary tool for working with biomolecular structures. The mmView application is offered in two flavors: as a publicly available web server http://ich.vscht.cz/projects/mmview/, and as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user’s computer. Petr Cech and Daniel Svozil -- Daniel Svozil, PhD Head of Laboratory of Informatics and Chemistry Institute of Chemical Technology Czech Republic phone: +420 220 444 391 http://ich.vscht.cz/~svozil -- gmx-users mailing listgmx-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
Re: [gmx-users] gromacs installation error
Hi, Thanks for the reply, I check the path and everything still I get this error. Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it! -Original Message- From: Javier Cerezo j...@um.es Sender: gmx-users-boun...@gromacs.org Date: Tue, 06 Dec 2011 13:30:55 To: Discussion list for GROMACS usersgmx-users@gromacs.org Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] gromacs installation error -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] dihedral format in top file?
Hi, I am inexperienced with gromacs and I would like to figure out the format of all parts of a .top file, needed for Gromacs. I am trying to understand the input format so I can write a program for automatic setup for small molecule ligands with Gromacs, using the oplsaa force field. I have recently written a C++ program that converts BOSS autoput and creates NAMD input. Now I would like to do a similar program for Gromacs. I would like to write as few files as possible. I have some problems understanding the format of the dihedrals in the .top file. I have pasted the top file for methanol I have been preparing manually below. Please point out any errors. Any pointers would be greatly appreciated. Methanol4 [atoms] 1 opls_157 1 UNK C00 1 -0.043617 2 opls_154 1 UNK O01 1 -0.586987 3 opls_156 1 UNK H02 1 0.074589 4 opls_156 1 UNK H03 1 0.074589 5 opls_156 1 UNK H04 1 0.074589 6 opls_155 1 UNK H05 1 0.406836 [bonds] 1 2 1 0.14100 267776.00 2 6 1 0.09450 462750.40 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 [angles] 4 1 2 1 109.50 292.880 5 1 2 1 109.50 292.880 6 2 1 1 108.50 460.240 3 1 2 1 109.50 292.880 4 1 5 1 107.80 276.144 5 1 3 1 107.80 276.144 5 1 4 1 107.80 276.144 [dihedrals] 6 2 1 3 3 ?? ... ?? If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how do I enter the information in the dihedral part of the .top file? The RB parameters for 6-2-1-3 is given below: C0 = 0.94140 C1 = 2.82420 C2 = 0.0 C3 = -3.76560 C4 = 0.0 C5 = 0.0 How do I enter this information into the .top file? Any help would be greatly appreciated! Thanks! Best, Markus -- gmx-users mailing listgmx-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
Re: [gmx-users] RE: logfile size
Not the main problem, but your dt=0.0002 (0.2fs), is it what you want? Javier El 06/12/11 15:59, Mark Abraham escribió: On 7/12/2011 12:12 AM, Mark Abraham wrote: On 6/12/2011 8:48 PM, lloyd riggs wrote: Dear All, Hope this is not tooo stupid a question. I recenttly reduced my file sizes by increasing the time between writing. However, if I do an Umbrella run I get the following to my logfile output, which makes my log file in the end larger than my trajectory; Dispersion correction V -5.49759e+03 dVdl 0.0e+00 Dispersion correction V -5.49756e+03 dVdl 0.0e+00 Dispersion correction V -5.49753e+03 dVdl 0.0e+00 Dispersion correction V -5.49750e+03 dVdl 0.0e+00 Dispersion correction V -5.49747e+03 dVdl 0.0e+00 Dispersion correction V -5.49744e+03 dVdl 0.0e+00 Dispersion correction V -5.49741e+03 dVdl 0.0e+00 Dispersion correction V -5.49738e+03 dVdl 0.0e+00 Dispersion correction V -5.49735e+03 dVdl 0.0e+00... Does anyone know how to turn this off for the logfile, I get one of these for each step, instead of for each write step? My write portion of the .mdp file is; nsteps = 2000 ; 2 * 5 = 100 ps dt = 0.0002 ; 2 fs tinit = 0 ; Output control nstxout = 10 ; save coordinates every 0.2 ps nstvout = 10 ; save velocities every 0.2 ps nstenergy = 10 ; save energies every 0.2 ps nstcalcenergy = 100 nstfout = 10 nstlog = 10 ; update log file every 0.2 ps nstxtcout = 10 Check out the list of options in mdrun -h. There's one that will completely stop this printing. I think it's supposed to print this stuff only according to nstlog, but the code is slightly broken here. I'll suggest a fix. Nah, the code looks fine - it should only ever print at nstlog steps. Mark -- Javier CEREZO BASTIDA Ph.D. Student Physical Chemistry Universidad de Murcia 30100, Murcia (SPAIN) T: (0034)868887434 -- gmx-users mailing listgmx-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
[gmx-users] intel grompp with pathscale mdrun
Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-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
RE: [gmx-users] dihedral format in top file?
Section 5.3.3 of the manual. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Markus K. Dahlgren Sent: Wednesday, 7 December 2011 4:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] dihedral format in top file? Hi, I am inexperienced with gromacs and I would like to figure out the format of all parts of a .top file, needed for Gromacs. I am trying to understand the input format so I can write a program for automatic setup for small molecule ligands with Gromacs, using the oplsaa force field. I have recently written a C++ program that converts BOSS autoput and creates NAMD input. Now I would like to do a similar program for Gromacs. I would like to write as few files as possible. I have some problems understanding the format of the dihedrals in the .top file. I have pasted the top file for methanol I have been preparing manually below. Please point out any errors. Any pointers would be greatly appreciated. Methanol4 [atoms] 1 opls_157 1 UNK C00 1 -0.043617 2 opls_154 1 UNK O01 1 -0.586987 3 opls_156 1 UNK H02 1 0.074589 4 opls_156 1 UNK H03 1 0.074589 5 opls_156 1 UNK H04 1 0.074589 6 opls_155 1 UNK H05 1 0.406836 [bonds] 1 2 1 0.14100 267776.00 2 6 1 0.09450 462750.40 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 [angles] 4 1 2 1 109.50 292.880 5 1 2 1 109.50 292.880 6 2 1 1 108.50 460.240 3 1 2 1 109.50 292.880 4 1 5 1 107.80 276.144 5 1 3 1 107.80 276.144 5 1 4 1 107.80 276.144 [dihedrals] 6 2 1 3 3 ?? ... ?? If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how do I enter the information in the dihedral part of the .top file? The RB parameters for 6-2-1-3 is given below: C0 = 0.94140 C1 = 2.82420 C2 = 0.0 C3 = -3.76560 C4 = 0.0 C5 = 0.0 How do I enter this information into the .top file? Any help would be greatly appreciated! Thanks! Best, Markus -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] itp file for D2O
Dear GROMACS users, I usually use spce.itp file for water solvent in my simulation. However, now I want to change this solvent to deuterium monoxide (D2O). Please let me know if I have to change this itp file? if yes, where can I find this file? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- gmx-users mailing listgmx-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
[gmx-users] Can Gromacs do Targeted MD simulation?
Hi all, Just as the title, can Gromacs do Targeted MD simulations? If Yes, how to set up the simulation procedure? -- gmx-users mailing listgmx-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
Re: [gmx-users] itp file for D2O
Hi, I think you simply use #include spce.itp in your topology file. Please see http://www.gromacs.org/Documentation/Include_File_Mechanism Thanks. Surya Prakash Tiwari On Tue, Dec 6, 2011 at 19:53, cuong nguyen nvcuon...@gmail.com wrote: Dear GROMACS users, I usually use spce.itp file for water solvent in my simulation. However, now I want to change this solvent to deuterium monoxide (D2O). Please let me know if I have to change this itp file? if yes, where can I find this file? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] itp file for D2O
Surya Prakash Tiwari On Tue, Dec 6, 2011 at 20:34, Justin A. Lemkul jalem...@vt.edu wrote: Surya Prakash Tiwari wrote: Hi, I think you simply use #include spce.itp in your topology file. Please see http://www.gromacs.org/Documentation/Include_File_Mechanism This will not give D2O - the SPC/E water model is for H2O. I would suggest to the OP to search for a suitable D2O model. I suspect there is one out there. I meant that he usually uses #include spce.itp for SPC/E water model. Sorry abt the confusion. -Justin Thanks. Surya Prakash Tiwari On Tue, Dec 6, 2011 at 19:53, cuong nguyen nvcuon...@gmail.com wrote: Dear GROMACS users, I usually use spce.itp file for water solvent in my simulation. However, now I want to change this solvent to deuterium monoxide (D2O). Please let me know if I have to change this itp file? if yes, where can I find this file? Thank you very much. Best regards, Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981 -- 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. 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 -- 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] intel grompp with pathscale mdrun
Should work just fine. As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.ne...@utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- 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 -- gmx-users mailing listgmx-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
[gmx-users] intel grompp with pathscale mdrun
Thank you Matthew. your suggestion for the hanging .o compilation sounds good. I didn't try it because in the end the intel compiler produced the fastest executables in any event. For those interested, here are my benchmarking speeds for one of my simulation systems (270,000 atoms) on 48 cores of an AMD magny-cours cluster at 2.1 GHz. I have no idea why the intel icc compiler outperforms the pathscale and pgi compilers on AMD computers, but that seems to be the case. intel icc 12.0.5.220 = 3.733 ns/day intel icc 12.0.5.220 with -msse3 = 3.765 ns/day pathscale 4.0.12.1 = 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.neale at utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Previous message: [gmx-users] intel grompp with pathscale mdrun Next message: [gmx-users] dihedral format in top file? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] -- gmx-users mailing listgmx-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
RE: [gmx-users] intel grompp with pathscale mdrun
Hi Chris, You can also try with open64. Let us know in case you face any issues in compiling and running. We will be glad to help you. Thanks Anupama -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of chris.ne...@utoronto.ca Sent: Wednesday, December 07, 2011 8:15 AM To: gmx-users@gromacs.org Subject: [gmx-users] intel grompp with pathscale mdrun Thank you Matthew. your suggestion for the hanging .o compilation sounds good. I didn't try it because in the end the intel compiler produced the fastest executables in any event. For those interested, here are my benchmarking speeds for one of my simulation systems (270,000 atoms) on 48 cores of an AMD magny-cours cluster at 2.1 GHz. I have no idea why the intel icc compiler outperforms the pathscale and pgi compilers on AMD computers, but that seems to be the case. intel icc 12.0.5.220 = 3.733 ns/day intel icc 12.0.5.220 with -msse3 = 3.765 ns/day pathscale 4.0.12.1 = 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale chris.neale at utoronto.ca wrote: Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask because I can only compile mdrun with the pathscale compiler because make install hangs while make install-mdrun works fine. make install is hanging on making g_rms.o as previously posted: http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I tried this again with the 4.0.12.1 version of the compiler and have the same result. Thank you, Chris. -- gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Previous message: [gmx-users] intel grompp with pathscale mdrun Next message: [gmx-users] dihedral format in top file? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
