[gmx-users] tfe.itp
Dear justin I made topology top for tfe with gromos53a5.and I solvated in spc and 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I get this error.(I edit the name of atoms with name in rtp file HT) Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file topol.top, line 57]: No default Proper Dih. types Cleaning up temporary file gromppsYSJRG --- Program grompp, VERSION 3.3.2 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'HO' not found! --- my topology file is attached. best -- sh-karbalaee topol.top Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] REMD trjcat -demux problem
Di Pan wrote: Hi, everyone: I met a problem when I try to use the trjcat -demux to connect trajectory files of REMD. I use 68 replicas for REMD simulation, and use demux.pl script to get the replica_index.vgx file. Then I try to use the trjcat -f traj*.xtc -demux replica_index.xvg to get a continuous trajctory file. But I got an error information as below: Fatal error: Demuxing the same replica 2 twice at time 32.00 My REMD sets the exchange time at every 2ps and record the coordinate information also at every 2ps. Check the index file at the line corresponding to 32 ps. Does it have the number 2 more than once? Was the index file meddled with, maybe transported from one computer to another? Does anyone meet the same problem or can give me some advice? I much appreciate any advice and help. Di,Pan Graduate Student at School of Engineering Department of Biomedical Engineering University of Alabama at Birmingham ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using Morse potentials with ENCAD force field
Andy Shelley wrote: I have added a mixture of oxgen and nitrogen to a simulation with a cnt. The oxygen and nitrogen use morse potentials and the cnt uses the encad force field. Previously I simulated the cnt with the default water and it worked well. When using my air mixture the cnt collapses even if a small number of molecules is added. The values I am using for the potentials are: N-N O-O b0 (nm);0.10980.1207 D (kJ mol-1);941.692 493.50 Beta(nm-1)26.42 26.80 Do these values seem right and is there anything I should be aware of with my setup? The morse bit could be right, but how about the non-bonded interactions between air and CNT? I don't understand why you would use Encad for the CNT either, although it may be quite similar to other force fields in practice. Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] flexible organic solvents
Hi, additionally to the remaks of Andreas there are some parameters in the GROMOS force field G53a5/6 for the solvents you want to simulate (see the original paper). A good read of chapter five of the manual and to all the files in the $GMX/share/top directory should let you build those models. Note there's also a decane.itp there, which uses the Ryckaert-Bellemans potential (as in Berger lipids). One comment on the chair to boat (or more exactly twist-boat) transition, the enthalpy barrier has been estimated to ~ 10 kcal/mol by ab initio and MM2 calculations. It is thus unlikely to observe any transition within a few nanoseconds if you start from a chair conformation at room temperature. Ciao, Patrick Kukol, Andreas a écrit : Yes that should be possible without big problems. The Gromacs manual and Wiki pages about how to build a topology is a good starting point. Then you could try the gromacs program x2top to generate a topology, or the Prodrg2 server. Andreas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sascha Rehm Sent: 14 August 2008 12:03 To: gmx-users@gromacs.org Subject: [gmx-users] flexible organic solvents Dear Gromacs users, I simulate proteins with different organic solvents like toluene, cyclohexane or isopentane. Right now, I used rigid body models for these solvents, made and simulated with Amber. For my future work, I unse Gromacs and need to rebuild these solvents. Can I build a cyclohexane model, which is more flexible and can change from chair conformation to boat conformation and vice versa? And how do I build a non-rigid Isopentane with internal degrees of freedom? Hope, this is not a stupid questions, but I searched quite a while the mailing list and also google, but did nearly find nothing about other common (flexible) solvents. Can someone give me a hint, which keywords I should use to search or where I can find some informations/tutorials/explanations? Thanks a lot, Sascha ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: [EMAIL PROTECTED] new postal address !!! Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INTS, INSERM UMR-S726, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31 Web Site: http://www.dsimb.inserm.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tfe.itp
shahrbanoo karbalaee wrote: Dear justin I made topology top for tfe with gromos53a5.and I solvated in spc and 40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I get this error.(I edit the name of atoms with name in rtp file HT) Generated 165 of the 1596 non-bonded parameter combinations ERROR 0 [file topol.top, line 57]: No default Proper Dih. types Cleaning up temporary file gromppsYSJRG --- Program grompp, VERSION 3.3.2 Source code file: toputil.c, line: 61 Fatal error: Atomtype 'HO' not found! --- my topology file is attached. In the topol.top you've provided, you define all the necessary components for TFE, but then later call tfe.itp. Why? You've obviously got an inconsistency somewhere. Think of it this way - in a topol.top for a protein generated by pdb2gmx, you don't generate all the protein parameters, then later on, call protein.itp within topol.top! If you just have a system of TFE + water, then you can define the TFE parameters at the beginning of the .top, then just call spc.itp later. I'm betting that within tfe.itp lies the problem. Remove the call for tfe.itp and see how it goes, because you've already defined everything you need. -Justin best ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FFTW Gromacs installation on AIX 5.3
Hi, Earlier i had faced problems installing FFTW on IBM p595. Thankfully now I had found out that they were already installed and I assumed they weren't: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.* -rw-r--r-- 1 applic in0007 2507094 Nov 12 2007 /applic/local/lib/libfftw3.a -rwxr-xr-x 1 applic in0007 766 Nov 12 2007 /applic/local/lib/libfftw3.la And here: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/include/fftw3.* -rw-r--r-- 1 applic in0007 2373 Nov 12 2007 /applic/local/include/fftw3.f -rw-r--r-- 1 applic in000714011 Nov 12 2007 /applic/local/include/fftw3.h I have added the following lines to my .bashrc: # for Gromacs export CPPFLAGS=-I/applic/local/include export LDFLAGS=-L/applic/local/lib export AR='ar -X 32' export CC='xlc_r -q32' export F77='xlf_r -q32' export CXX='xlC_r -q32' export OBJECT_MODE=32 export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export FFLAGS='-O4 -qmaxmem=-1 -qstrict' export CFLAGS='-O4 -qmaxmem=-1 -qstrict' export MPICC=mpicc After that, I do: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333 result I get the following: configure: WARNING: unknown Fortran name-mangling scheme ./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found And a grep for fftw in the file result yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw result checking for fftw3.h... yes checking for main in -lfftw3f... yes And tail result gives: [EMAIL PROTECTED]:~/gromacs-3.3.3$ tail result config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands And a grep for fftw in the config.log file yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw config.log configure:25588: checking for fftw3.h configure:25636: checking for main in -lfftw3f configure:25673: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26248: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26323: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26423: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26593: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26688: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26818: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26920: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27206: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lX11 -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27456: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm -lX11 5 1586-403 (E) Library file fftw3f not found. configure:27699: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27947: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28114: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28281: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28436: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lICE -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not
Re: [gmx-users] FFTW Gromacs installation on AIX 5.3
We recently ran into this issue, and it was solved by re-compiling FFTW in single precision. I would suggest talking to your sysadmin to see if you can get the right precision compiled. Not a bad idea to have both single and double precision available to you, anyway :) -Justin Senthil Kumar M wrote: Hi, Earlier i had faced problems installing FFTW on IBM p595. Thankfully now I had found out that they were already installed and I assumed they weren't: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.* -rw-r--r-- 1 applic in0007 2507094 Nov 12 2007 /applic/local/lib/libfftw3.a -rwxr-xr-x 1 applic in0007 766 Nov 12 2007 /applic/local/lib/libfftw3.la And here: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/include/fftw3.* -rw-r--r-- 1 applic in0007 2373 Nov 12 2007 /applic/local/include/fftw3.f -rw-r--r-- 1 applic in000714011 Nov 12 2007 /applic/local/include/fftw3.h I have added the following lines to my .bashrc: # for Gromacs export CPPFLAGS=-I/applic/local/include export LDFLAGS=-L/applic/local/lib export AR='ar -X 32' export CC='xlc_r -q32' export F77='xlf_r -q32' export CXX='xlC_r -q32' export OBJECT_MODE=32 export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export FFLAGS='-O4 -qmaxmem=-1 -qstrict' export CFLAGS='-O4 -qmaxmem=-1 -qstrict' export MPICC=mpicc After that, I do: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333 result I get the following: configure: WARNING: unknown Fortran name-mangling scheme ./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found And a grep for fftw in the file result yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw result checking for fftw3.h... yes checking for main in -lfftw3f... yes And tail result gives: [EMAIL PROTECTED]:~/gromacs-3.3.3$ tail result config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands And a grep for fftw in the config.log file yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw config.log configure:25588: checking for fftw3.h configure:25636: checking for main in -lfftw3f configure:25673: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26248: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26323: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26423: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26593: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26688: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26818: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26920: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27206: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lX11 -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27456: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm -lX11 5 1586-403 (E) Library file fftw3f not found. configure:27699: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27947: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28114: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28281: xlc_r -q32 -o conftest -O4 -qmaxmem=-1
Re: [gmx-users] New Gromacs-CPMD QMMM webpage
dear sir, i am vidhya sankar speaking . i am not able to down load QM/MM exampiles files since it take much time and huge memory (156Mb) often net is disconnected could you please send some example input files of CPMD part mainly 'CPMD_inp.tmpl' 'runcpmd' ? please i am expecting your reply soon --- On Fri, 15/8/08, Pradip Biswas [EMAIL PROTECTED] wrote: From: Pradip Biswas [EMAIL PROTECTED] Subject: [gmx-users] New Gromacs-CPMD QMMM webpage To: gmx-users@gromacs.org Date: Friday, 15 August, 2008, 4:41 AM Dear Users, The modified Gromacs code for Gromacs-CPMD QMMM is now available at: http://www.tougaloo.edu/research/qmmm/ Please note that we fixed a bug related to MM layering in the version gmx-3.3.1_qmmm-1.3.1 and uploaded a new version, gmx-3.3.1_qmmm-1..3.2. If you are using version 1.3.1, you should upgrade to v-1.3.2 or contact us ([EMAIL PROTECTED]) to fix the typos in v-1.3.1. The site http://comppsi.csuohio.edu/groups/qmmm.html is offline because of lab renovation and will not be maintained hereafter. The Gromacs-CPMD page will henceforth be continued in the above mentioned site. Cheers, Pradip K Biswas. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Add more friends to your messenger and enjoy! Go to http://in.messenger.yahoo.com/invite/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MDRUN with MPIRUN
Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody can give the exact command to run mdrun with MPI. It will be of great help for me to do my job. Thanks in advance, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FFTW Gromacs installation on AIX 5.3
Hi Senthil,
here is how I have compiled fftw and gromacs on an AIX. A warning though that
the gromacs compilation usin the xlc_r compiler set took over 12h.
First fftw:
[EMAIL PROTECTED]:/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix cat cn_compile.sh
#!/bin/bash
export
PATH=/usr/vac/bin:/usr/vacpp/bin:/opt/freeware:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:.:/tools/local/bin
export F77=xlf_r
export CC=xlc_r
export CXX=xlc++_r
export FFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
export CFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
export CXXFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
## modify kernel/cycle.h
## replace all inline with __inline__
MD=/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix
cd ${MD}
mkdir exec
export FFTW_LOCATION=${MD}/exec
./configure --enable-float --enable-threads --prefix=${FFTW_LOCATION}
output.configure 21
make output.make 21
make install output.make_install 21
make distclean
touch DONE_SINGLE
./configure --enable-threads --prefix=${FFTW_LOCATION}
output.configure_d 21
make output.make_d 21
make install output.make_install_d 21
make distclean
##
Now gromacs:
#!/bin/bash
export
PATH=/usr/vac/bin:/usr/vacpp/bin:/opt/freeware:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:.:/tools/local/bin
export F77=xlf_r
export CC=xlc_r
export CXX=xlc++_r
export FFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
export CFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
export CXXFLAGS=-O5 -qarch=pwr6 -qtune=pwr6
export FFTW_LOCATION=/hpf/data/pomes/cneale/exe/fftw-3.1.2_aix/exec
export GROMACS_LOCATION=/hpf/data/pomes/cneale/exe/gromacs-3.3.1_aix/exec
export CPPFLAGS=-I$FFTW_LOCATION/include
export LDFLAGS=-L$FFTW_LOCATION/lib
cd /hpf/data/pomes/cneale/exe/gromacs-3.3.1_aix
mkdir exec
./configure --prefix=$GROMACS_LOCATION output.configure 21
make output.make 21
make install output.make_install 21
make distclean
touch DONE_SERIAL
echo cn-r0-10 ~/.rhosts
echo localhost ~/host.list
for((i=2;i=16;i++)); do
echo localhost ~/host.list
done
export MP_HOSTFILE=~/host.list
./configure --prefix=$GROMACS_LOCATION --enable-mpi --disable-nice
--program-suffix=_mpi CC=mpcc_r F77=mpxlf_r output.configure_mpi
21
make mdrun output.make_mpi 21
make install-mdrun output.make_install_mpi 21
make distclean
#
Hope it helps,
Chris.
Hi,
Earlier i had faced problems installing FFTW on IBM p595. Thankfully
now I had found out that they were already installed and I assumed
they weren't:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.*
-rw-r--r-- 1 applic in0007 2507094 Nov 12 2007
/applic/local/lib/libfftw3.a
-rwxr-xr-x 1 applic in0007 766 Nov 12 2007
/applic/local/lib/libfftw3.la
And here:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/include/fftw3.*
-rw-r--r-- 1 applic in0007 2373 Nov 12 2007
/applic/local/include/fftw3.f
-rw-r--r-- 1 applic in000714011 Nov 12 2007
/applic/local/include/fftw3.h
I have added the following lines to my .bashrc:
# for Gromacs
export CPPFLAGS=-I/applic/local/include
export LDFLAGS=-L/applic/local/lib
export AR='ar -X 32'
export CC='xlc_r -q32'
export F77='xlf_r -q32'
export CXX='xlC_r -q32'
export OBJECT_MODE=32
export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'
export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'
export FFLAGS='-O4 -qmaxmem=-1 -qstrict'
export CFLAGS='-O4 -qmaxmem=-1 -qstrict'
export MPICC=mpicc
After that, I do:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333
result
I get the following:
configure: WARNING: unknown Fortran name-mangling scheme
./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found
And a grep for fftw in the file result yields:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw result
checking for fftw3.h... yes
checking for main in -lfftw3f... yes
And tail result gives:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ tail result
config.status: creating share/template/Makefile
config.status: creating share/top/Makefile
config.status: creating share/html/Makefile
config.status: creating share/html/images/Makefile
config.status: creating share/html/online/Makefile
config.status: creating man/Makefile
config.status: creating man/man1/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
And a grep for fftw in the config.log file yields:
[EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw config.log
configure:25588: checking for fftw3.h
configure:25636: checking for main in -lfftw3f
configure:25673: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
-I/applic/local/include -L/applic/local/lib conftest.c -lfftw3f -lm
5
1586-403 (E) Library file fftw3f not found. configure:26248: xlc_r
-q32 -o conftest -O4 -qmaxmem=-1 -qstrict
-I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f
-lm 5
1586-403 (E) Library file fftw3f not found.
configure:26323: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict
Re: [gmx-users] FFTW Gromacs installation on AIX 5.3
ls -l /applic/local/lib/libfftw* should see libfftw3f.a there (libfftw3.a is the double precision, libfftw3f.a is the single precision fftw3 lib) export LIBS='-L/applic/local/lib -lfftw3f' ./configure ... Senthil Kumar M wrote: Hi, Earlier i had faced problems installing FFTW on IBM p595. Thankfully now I had found out that they were already installed and I assumed they weren't: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/lib/libfftw3.* -rw-r--r-- 1 applic in0007 2507094 Nov 12 2007 /applic/local/lib/libfftw3.a -rwxr-xr-x 1 applic in0007 766 Nov 12 2007 /applic/local/lib/libfftw3.la And here: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ls -al /applic/local/include/fftw3.* -rw-r--r-- 1 applic in0007 2373 Nov 12 2007 /applic/local/include/fftw3.f -rw-r--r-- 1 applic in000714011 Nov 12 2007 /applic/local/include/fftw3.h I have added the following lines to my .bashrc: # for Gromacs export CPPFLAGS=-I/applic/local/include export LDFLAGS=-L/applic/local/lib export AR='ar -X 32' export CC='xlc_r -q32' export F77='xlf_r -q32' export CXX='xlC_r -q32' export OBJECT_MODE=32 export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict' export FFLAGS='-O4 -qmaxmem=-1 -qstrict' export CFLAGS='-O4 -qmaxmem=-1 -qstrict' export MPICC=mpicc After that, I do: [EMAIL PROTECTED]:~/gromacs-3.3.3$ ./configure --prefix=$HOME/GROMACS333 result I get the following: configure: WARNING: unknown Fortran name-mangling scheme ./configure[24445]: ACX_FIXED_FUNC_FSEEKO: not found And a grep for fftw in the file result yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw result checking for fftw3.h... yes checking for main in -lfftw3f... yes And tail result gives: [EMAIL PROTECTED]:~/gromacs-3.3.3$ tail result config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands And a grep for fftw in the config.log file yields: [EMAIL PROTECTED]:~/gromacs-3.3.3$ grep fftw config.log configure:25588: checking for fftw3.h configure:25636: checking for main in -lfftw3f configure:25673: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26248: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26323: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26423: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26593: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26688: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26818: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:26920: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27206: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lX11 -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27456: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm -lX11 5 1586-403 (E) Library file fftw3f not found. configure:27699: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:27947: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28114: xlc_r -q32 -o conftest -O4 -qmaxmem=-1 -qstrict -I/applic/local/include -L/applic/local/lib conftest.c -lnsl -lfftw3f -lm 5 1586-403 (E) Library file fftw3f not found. configure:28281:
RE: [gmx-users] MDRUN with MPIRUN
mpirun -np number of processors mdrun various options... -np number of processors (all in one line) From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma Sent: 20 August 2008 12:44 To: Discussion list for GROMACS users Subject: [gmx-users] MDRUN with MPIRUN Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody can give the exact command to run mdrun with MPI. It will be of great help for me to do my job. Thanks in advance, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MDRUN with MPIRUN
Hi, Thanks for your reply. Do you have any idea of how to run commands using scheduler command bsub With Thanx, Vivek 2008/8/20 Kukol, Andreas [EMAIL PROTECTED] mpirun -np number of processors mdrun various options... -np number of processors (all in one line) From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of vivek sharma Sent: 20 August 2008 12:44 To: Discussion list for GROMACS users Subject: [gmx-users] MDRUN with MPIRUN Hi There, I am trying to run the gromacs with mpirun, but don't know the exact commands for running gromacs with mpirun. If, somebody can give the exact command to run mdrun with MPI. It will be of great help for me to do my job. Thanks in advance, Vivek ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using Morse potentials with ENCAD force field
Actually I think I am using the gromos force field. I have been using Christopher Stiles page as a guide to get started with using CNT http://cs86.com/CNSE/SWNT.htm. I realize now that all the modifications were made to ffgmx files. So I believe I am using the gromos forcefield. Is the forcefield used defined by the parameters? I have added nonbonded parameters to ffgmxnb.itp as the following: [ nonboned_params ] ON1 0.00691.4016E-05 OO1 0.00619.9676E-06 NN1 0.00761.8778E-05 CO1 0.00304.7908E-06 CN1 0.00336.5271E-06 and the same for pairtypes [ pairtypes ] CN1 0.0033 6.5271E-06 CO1 0.0030 4.7908E-06 NN1 0.0076 1.8778E-05 OO1 0.0061 9.9676E-06 ON1 0.0069 1.4016E-05 I have put just 200 nitrogen molecules in a 24.7nm x 24.7nm x 12.3nm box with a 10,10 cnt length 12.3nm. The nitrogen molecules appear to not even interact with the cnt but it still flattens. Any ideas? Thanks, Andy ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulations backward in time.
Hi, I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? Thanks Sumanth N Jamadagni Graduate Student Isermann Dept of Chemical and Biological Engg Rensselaer Polytechnic Institute ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tfe.itp
Dear justin after edit tfe.itp , I did the command grompp and I got this error : error input solvated.gro. Do I have to make spc.gro with tis forcefield(gromos965a)? best -- sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
