[gmx-users] itp files in membrane simulation
Dear all, I want to use lipid.itp dmpc.itp for a bilayer simulation, and I have gathered this information so far that one has to manually modify these itp files in order to use the latest force fields, ie, G43a2 etc. Does this include lipid.itp file too which involves various lipid-GROMOS interactions? Also, is there any command or program which when applied carries out the required combination rules for evaluating lipid-GROMOS interactions or that also has to be done manually!! I shall be highly thankful to you all, regards, Priyanka S. Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] membrane set up!!!
The below-mentioned lines (from forum) do not work for me!! I am dealing with DMPC instead of POPC and I hope that is not making any difference!! kindly help, Priyanka S. Hu Ugur, actually you don't have to care to run the lipid pdb by Tieleman through pdb2gmx at all - just copy the respective lines out of lipid.itp into ffG43a1bon.itp and ffG43a1nb.itp (or the force field you want to use) and put #include pope.itp into your *.top file - et voila, you're done. Attention: the lipid parameters are optimized to be used with SPC water! So pay attention when using TIP3... Greetings Steffen Need Mail bonding? Go to the Yahoo! Mail QA for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=listsid=396546091 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] problem still lies regarding dssp
Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance. regards SANGEETA - Heres a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] problem still lies regarding dssp
Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To find out use: ls -l /directory/where/you/put/dssp If you see any restricton to file permission change it to chmod a+rx dssp Hope this will help. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Fri 09/02/2007 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] problem still lies regarding dssp Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500 (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance. regards SANGEETA - Here's a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] loss of information trr xtc
hi guys. can anyone tell me if there is a loss of information when i convert a trr file into a less-storage-consuming xtc file ? can i reconevrt the xtc file into trr again and then have no loss of information ? thanks for a very short answer Greetings Joern ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] problem still lies regarding dssp
sangeeta kundu wrote: Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be never ending, intermediate files are prepared for some time, but I never got any .xpm files, I can not understand whether my system is not working, or I am making any mistake, but all the other programs of Gromacs like pdb2gmx, editconf , genbox, grompp, mdrun etc are going on successfully, problem lies only in case of dssp, I was suggested by Mark to try dssp independently on a single snapshot extracted from the trajectory, I took the snapshot of the protein after 500ps with the command *trjconv -f md.xtc -s md.tpr -o time_500ps.pdb -dump 500* (I think the command is correct, if not I earnestly request you to rectify my mistake), When I ran do_dssp on this single structure I waited for 3 days, but it did not finish and seems to be neverending, then I killed the program, In order to get that particular coloured plot of secondary structure vs time which method should I adopt? Seeking your help and thanks in advance. It sounds like do_dssp is having problems calling dssp. We can't help you much further. Try a new computer system, or work out a way to call dssp by hand for the structures you care about. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Pressure coupling question
Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine. After about 1ps, the system is near the reference temperature, and the oscillations are only about 1 or 2 degrees. So, I expected something, roughly, similar with the pressure. For the pressure, however, my reference pressure is 1.0 bar, but the pressure in the system after a few picoseconds seems to range from -400 to 400 bar. Is this normal? Do I just need to wait longer? Does this mean that I did not run the energy minimization long enough and there are some high forces? Is there something else that I am doing wrong? In my mdp file, the pressure coupling looks like: Pcoupl = berendsen Pcoupltype = isotropic tau_p= 0.5 compressibility = 4e-5 ref_p= 1.0 I have also tried Parrinello-Rahman pressure coupling with the same result. Thanks Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Pressure coupling question
toma0052 wrote: Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine. After about 1ps, the system is near the reference temperature, and the oscillations are only about 1 or 2 degrees. So, I expected something, roughly, similar with the pressure. For the pressure, however, my reference pressure is 1.0 bar, but the pressure in the system after a few picoseconds seems to range from -400 to 400 bar. Is this normal? Do I just need to wait longer? Does this mean that I did not run the energy minimization long enough and there are some high forces? Is there something else that I am doing wrong? In my mdp file, the pressure coupling looks like: Pcoupl = berendsen Pcoupltype = isotropic tau_p= 0.5 compressibility = 4e-5 ref_p= 1.0 I have also tried Parrinello-Rahman pressure coupling with the same result. Thanks Mike ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 this is normal. increase your system size to reduce the fluctuations. scales as sqrt(n) :(. -- 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 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] gromacs-3.3 build on linux. make fails
Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = here's my env: LDFLAGS=-L/usr/local/fftw301/lib CPPFLAGS=-I/usr/local/fftw301/include LD_LIBRARY_PATH=/usr/local/fftw301-double/lib CC=/usr/bin/gcc4 PATH=/usr/local/fftw301-double/lib/:/usr/local/fftw301-double/include:/usr/local/lam/7.1.2-gcc4/bin:/usr/kerberos/sbin: /usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/usr/local/lam/7.1.2-gcc4/: /usr/local/lam/7.1.2-gcc4/bin/ CAN SOMEONE HELP? what am I missing? thank you. Susan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Urey bradley term in the sum of energies
Hello everybody, I've got an awful doubt on how the Urey-Bradley (UB) term is taken into account in the potential energy. When an angle has got regular and UB parameters, how this will appear in the .edr file? The angle energy will only appear in the UB term only or it will be splitted between Angle and UB terms? I guess that both parameters are used in the computation but I'm not sure whether they are added before be printed in the .edr file or not. Thanks Nicolas -- [ Nicolas Sapay Ph.D. ] University of Calgary, Dept. of Biological Sciences 2500 University Dr. NW, Calgary AB, T2N 1N4, Canada Tel: (403) 220-6869 Fax: (403) 289-9311 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Urey bradley term in the sum of energies
Nicolas SAPAY wrote: Hello everybody, I've got an awful doubt on how the Urey-Bradley (UB) term is taken into account in the potential energy. When an angle has got regular and UB parameters, how this will appear in the .edr file? If you have a force field with both angle function 1 and angle function 5 (IIRC, for U-B) defined for the same set of 3 atoms, then to the best of my knowledge, GROMACS will do both blithely and the output will go into Angles and U-B in the expected fashion. Certainly this happens when such functions are defined for different sets of 3 atoms. Note that from GROMACS point of view, the U-B term includes both the angle stretch and the harmonic position stretch. CHARMM the program lists only the latter as U-B. The angle energy will only appear in the UB term only or it will be splitted between Angle and UB terms? I guess that both parameters are used in the computation but I'm not sure whether they are added before be printed in the .edr file or not. I'm not quite sure what you're asking, but the structure of the bonded interaction code is such that all of the angle functions of type 1 will contribute only to Angles and all of the angle functions of type 5 will contribute only to U-B. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gromacs-3.3 build on linux. make fails
susan james wrote: Hello, I'm new to this list and hope I can get some help. Thanks for the good help request - lots of pertinent information can only improve your chances of getting help! the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = Unfortunately about another twenty lines of this will probably be instructive - you've actually cut off part of the command that failed. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] gromacs-3.3 build on linux. make fails
susan james wrote: Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = for some reason it did not compile the assembly bits. it could be due to gcc4, or maybe because you did a single precision compilation first. in the latter case try make distclean before running configure. -- 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 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] gromacs-3.3 build on linux. make fails
here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this? == . . . if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\/usr/local/gromacs-double/3.3/share/top\ -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT toputil.o -MD -MP -MF .deps/toputil.Tpo -c -o toputil.o toputil.c; \ then mv -f .deps/toputil.Tpo .deps/toputil.Po; else rm -f .deps/toputil.Tpo; exit 1; fi if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\/usr/local/gromacs-double/3.3/share/top\ -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT topdirs.o -MD -MP -MF .deps/topdirs.Tpo -c -o topdirs.o topdirs.c; \ then mv -f .deps/topdirs.Tpo .deps/topdirs.Po; else rm -f .deps/topdirs.Tpo; exit 1; fi if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\/usr/local/gromacs-double/3.3/share/top\ -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c; \ then mv -f .deps/grompp.Tpo .deps/grompp.Po; else rm -f .deps/grompp.Tpo; exit 1; fi /bin/sh ../../libtool --mode=link --tag=CC mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/usr/local/fftw301/lib -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -L/usr/X11R6/lib64 -lnsl -lfftw3 -lm -lSM -lICE -lX11 mkdir .libs mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o -L/usr/local/fftw301/lib ../mdlib/.libs/libmd_mpi_d.so -L/usr/X11R6/lib64 -L/usr/local/fftw301-double/lib ../gmxlib/.libs/libgmx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = David van der Spoel wrote: susan james wrote: Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving
Re: [gmx-users] gromacs-3.3 build on linux. make fails
susan james wrote: here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this? you do want to use mpicc which gives you all the libraries and include paths. but please check whether you have another gcc installed, or what the default gcc is (gcc -V). You can usually set a variable like MPICC=gcc3 if you have an executable gcc3 somewhere. by the way, your log snippet did not have the info from compiling the src/gmxlib/nonbonded directory, where something went wrong, apparently -- 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 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
