Re: [gmx-users] trjcat -settime option
Hi, It seems that you got two questions: 1. concat several trajectory together, use trjcat. 2. use tpbconv. To use tpbconv, just use the last trajectory you have before the computer failure. Also, to use tpbconv, you will need edr. I suggest you to use gmxcheck to check both the trr and edr file to find their common ending point. Yang Ye [EMAIL PROTECTED] wrote: Hello, again I'm sorry I had a mistake about my question. When using tpbconv command to make a new topol.tpr and continue a simulation due to some computer problems(e.g. power failure), should I select _l_ option? When I change confout.gro into conf.gro and continue a simulation, should I select _c_ option? Best Regards, Masa -- Masaomi Hatakeyama Ph.D Candidate(Knowledge Science, JAIST) [EMAIL PROTECTED] From: [EMAIL PROTECTED] Subject: [gmx-users] trjcat -settime option Date: Wed, 19 Apr 2006 12:57:28 +0900 (LDT) Hi everyone, I'd like to ask a easy question today. (I didn't understand the command explanation because of my poor english skill) Please teach me the difference c(continue) and l(last) when using -settime option with trjcat command. I have several trajectory files and want to conbine them, but I have two types. one of them: changing confout.gro into conf.gro and continue the simulation. the other: using tpbconv command to make a new topol.tpr due to some computer problems and continue the simulation. When using tpbconv command to make a new topol.tpr and continue a simulation due to some computer problems(e.g. power failure), should I use -l option? When I change confout.gro into conf.gro and continue a simulation, should I use -o option? If I don't use -settime option, what happen? Thanks in advance, Masa -- Masaomi Hatakeyama Ph.D Candidate(Knowledge Science, JAIST) [EMAIL PROTECTED] ___ 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 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 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] HOWTO for installing non-MPI gromacs-3.3.1 on cygwin
Hi Mark, Thanks! However, if you drop me a line with the exact names of the FFTW3 libraries/objects you were talking about I'll see if I can fix the autodetection script. Cheers, ERik On Apr 19, 2006, at 4:26 AM, Mark Abraham wrote: Hi, I recently re-installed gromacs 3.3.1 on a Windows XP machine running Cygwin and thought I would post a HOWTO since it has been of interest. If you want MPI, you're on your own. The Cygwin package of fftw3 doesn't name objects using the convention gromacs needs, so you'll have to build them yourself following the instructions below, derived from the gromacs installation guide. If you've installed the fftw3 package, it'll be best to uninstall it using the Cygwin installer (to prevent it downloading and installing updated packages, choose Install from Local Directory) 1. Get gromacs-3.3.1.tar.gz and fftw-3.0.1.tar.gz 2. Unpack the fftw distribution, cd to that directory and issue ./ configure --enable-threads --enable-sse --enable-float then make and make install 3. Uninstall previous versions of gromacs 4. Unpack the gromacs distribution, cd to that directory, apply any bug patches announced on the mailing list, and issue ./configure -- enable-shared LDFLAGS='-L/usr/local/lib' (If you've installed the cygwin lapack package, add --with-external-blas --with-external- lapack and change to LDFLAGS='-L/usr/local/lib -llapack -lblas'. If you've installed another lapack or blas then adjust LDFLAGS accordingly. If you don't know what lapack or blas are then ignore this.) 5. Now make and if all goes well, make install and make links 6. Edit your login files to add /usr/local/gromacs/man to the MANPATH and check that /usr/local/bin is in the PATH If you want double version of gromacs with double fftw then you will need to configure fftw with threads, sse2 and not float, then do make and make install, and then for gromacs make distclean configure as above plus enable double, etc. Hope this helps! 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 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] trjcat -settime option
Thanks for quick reply, Yang Ye and David, But my way of asking seemed not good. I know what trjcat command is. It is to concatinate two .trr files. but when we use trjcat command with -settime option, the command says as following, c (continue) - The start time is taken from the end of the previous file. Use it when your continuation run restarts with t=0. l (last) - The time in this file will be changed the same amount as in the previous. Use it when the time in the new run continues from the end of the previous one, since this takes possible overlap into account. I am confused which option I should use, either c or l. We usually, I think, continue the simulation as changing confout.gro to conf.gro, using grompp to make a new .tpr file, and mdrun. As a result, we have two .trr files. In this case, when we concatinate two .trr files, using trjcat command with -settime, we should select c(continue), right? On the other hand, Due to some computer failure, we usually use tpbconv command in order to continue the simulation as Yang and David said. In this case, after the simulation, when we concatinate two .trr files, using trjcat command with -settime, should we select l(last)? Is this correct? Sorry for bothering you, but I appreciate you if you answer my question. Best regards, Masa -- Masaomi Hatakeyama Ph.D Candidate(Knowledge Science, JAIST) [EMAIL PROTECTED] http://www.jaist.ac.jp/~m-hatake From: Yang Ye [EMAIL PROTECTED] Subject: Re: [gmx-users] trjcat -settime option Date: Wed, 19 Apr 2006 14:40:09 +0800 Hi, It seems that you got two questions: 1. concat several trajectory together, use trjcat. 2. use tpbconv. To use tpbconv, just use the last trajectory you have before the computer failure. Also, to use tpbconv, you will need edr. I suggest you to use gmxcheck to check both the trr and edr file to find their common ending point. Yang Ye [EMAIL PROTECTED] wrote: Hello, again I'm sorry I had a mistake about my question. When using tpbconv command to make a new topol.tpr and continue a simulation due to some computer problems(e.g. power failure), should I select _l_ option? When I change confout.gro into conf.gro and continue a simulation, should I select _c_ option? Best Regards, Masa -- Masaomi Hatakeyama Ph.D Candidate(Knowledge Science, JAIST) [EMAIL PROTECTED] From: [EMAIL PROTECTED] Subject: [gmx-users] trjcat -settime option Date: Wed, 19 Apr 2006 12:57:28 +0900 (LDT) Hi everyone, I'd like to ask a easy question today. (I didn't understand the command explanation because of my poor english skill) Please teach me the difference c(continue) and l(last) when using -settime option with trjcat command. I have several trajectory files and want to conbine them, but I have two types. one of them: changing confout.gro into conf.gro and continue the simulation. the other: using tpbconv command to make a new topol.tpr due to some computer problems and continue the simulation. When using tpbconv command to make a new topol.tpr and continue a simulation due to some computer problems(e.g. power failure), should I use -l option? When I change confout.gro into conf.gro and continue a simulation, should I use -o option? If I don't use -settime option, what happen? Thanks in advance, Masa -- Masaomi Hatakeyama Ph.D Candidate(Knowledge Science, JAIST) [EMAIL PROTECTED] ___ 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 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 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 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] FFTW installation error: cannot compile a simple Fortran program
Hi, I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: $ rpmbuild --rebuild fftw3-3.0.1-4.src.rpm GNU Fortran 3.2.3 g77 is available in the system. However, the installation fails with the error in Fortran compilation: ... ... checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... no checking whether g77 accepts -g... yes checking how to get verbose linking output from g77... configure: WARNING: compilation failed checking for Fortran 77 libraries... checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... configure: error: cannot compile a simple Fortran program See `config.log' for more details. error: Bad exit status from /var/tmp/rpm-tmp.15046 (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.15046 (%build) I would be grateful if anyone has any idea on how to solve the error. Thanks Sunny _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ 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] Paralellization limit?
Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the problem is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the master and continue only on the last two slaves (4 cpus, the systems are dual xeon). The problem is that I can't find any error message on the log files. I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6 and 8 cpus. So my question is: is there a limit of parallelization in gromacs depending on the simulated system? I'm using gromacs 3.3.1, mpich 1.2.5.2 and fftw 2.1.5. Thanks in advance Andrea ___ 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] FFTW installation error: cannot compile a simple Fortran program
hi On Wednesday 19 April 2006 13:16, Ge Sunny wrote: Hi, I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: $ rpmbuild --rebuild fftw3-3.0.1-4.src.rpm GNU Fortran 3.2.3 g77 is available in the system. However, the installation fails with the error in Fortran compilation: ... ... checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... no checking whether g77 accepts -g... yes checking how to get verbose linking output from g77... configure: WARNING: compilation failed checking for Fortran 77 libraries... checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... configure: error: cannot compile a simple Fortran program See `config.log' for more details. error: Bad exit status from /var/tmp/rpm-tmp.15046 (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.15046 (%build) I would be grateful if anyone has any idea on how to solve the error. Your system don`t have any working fortran compiler, reinstall it, or try another compiler like Intel icc and ifc. Have you tried to compile normal source code, does it work, or any other fortran code? Thanks Sunny _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- pgp8LicEgMmYV.pgp Description: PGP signature ___ 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] Paralellization limit?
Hi Andrea, Andrea Carotti wrote: Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the problem is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the master and continue only on the last two slaves (4 cpus, the systems are dual xeon). The problem is that I can't find any error message on the log files. I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6 and 8 cpus. So my question is: is there a limit of parallelization in gromacs depending on the simulated system? I'm using gromacs 3.3.1, mpich 1.2.5.2 and fftw 2.1.5. I have encountered similar problems when using mpich 1.2.x on Ethernet. Upgrading to mpich-2.x or using LAM solved the problems. There is only a parallelisation limit in the sense that using more CPUs does not always result in faster execution. 56 k atoms should run happily on 8 CPUs. Good luck, Carsten ___ 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] FFTW installation error: cannot compile a simple Fortran program
Florian Haberl wrote: hi On Wednesday 19 April 2006 13:16, Ge Sunny wrote: Hi, I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? Your system don`t have any working fortran compiler, reinstall it, or try another compiler like Intel icc and ifc. Have you tried to compile normal source code, does it work, or any other fortran code? Florian's advice seems sound to me. gfortran 4.0 is also an option - I recall there was some ugliness at the time FC4 was packaged that meant that the version of g77 was much earlier than gcc but I haven't needed to explore that further. 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] Paralellization limit?
Andrea Carotti wrote: Hi Carsten, thanks for your quick reply. Could you plese confrim me that gromacs 3.3.1 works and compile fine with mpich 2.x? Yes, compiles and runs in parallel. Only difference is that I use the FFTW3. Carsten Cause this is the first time that I hear that from a user and I'll go ahead on this way instead of usin LAM. Thanks again Andrea ___ 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] FFTW installation error: cannot compile a simple Fortran program
To Florian Haberl: I've also tried installing from fftw-3.0.1.tar.gz. Running ./configure can find g77, but another error appears as rdft/codelets/hc2r/Makefile.in not found: checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking how to get verbose linking output from g77... -v checking for Fortran 77 libraries... -L/usr/lib64 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../../lib64 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, extra underscore configure: creating ./config.status config.status: creating Makefile config.status: creating support/Makefile config.status: creating genfft/Makefile config.status: creating genfft-k7/Makefile config.status: creating kernel/Makefile config.status: creating simd/Makefile config.status: creating dft/Makefile config.status: creating dft/codelets/Makefile config.status: creating dft/codelets/standard/Makefile config.status: creating dft/codelets/inplace/Makefile config.status: creating dft/simd/Makefile config.status: creating dft/simd/codelets/Makefile config.status: creating dft/k7/Makefile config.status: creating dft/k7/codelets/Makefile config.status: creating rdft/Makefile config.status: creating rdft/codelets/Makefile config.status: creating rdft/codelets/r2hc/Makefile config.status: creating rdft/codelets/hc2r/Makefile config.status: error: cannot find input file: rdft/codelets/hc2r/Makefile.in To Mark: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? There is another problem. I'm not root. Running from binary pack has an error: error: can't create transaction lock on /var/lib/rpm/__db.000 I have tried creating .rpcmacros and all ./rpm subdirectories under my home directory, then run rpm. The error above still occurs. Sunny _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ 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] Re: LINCS Warning with MDRUN - Segmentation Fault (Gaurav Chopra)
Hi Attached is part of the gro file which gave the LINCS error on atoms. This output is the gro file for the initial mdrun, after which final grompp and final mdrun was done, which gives the error I described in the message below. Gaurav Gaurav Chopra wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice.you need to minimize better, but if your structures are really bad itwon't help either (e.g. when you have a sidechain sticking through a ring) --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, Swedenphone:46 18 471 4205fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se The lincs warnning are on water molecules isn't it ???XAvier Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water 49GLU HB2 797 4.183 3.686 4.460 49GLU CG 798 4.026 3.813 4.538 49GLU HG1 799 4.042 3.915 4.502 49GLU HG2 800 3.919 3.800 4.550 49GLU CD 801 4.094 3.805 4.672 49GLU OE1 802 4.149 3.697 4.707 49GLU OE2 803 4.086 3.910 4.737 49GLU C 804 4.170 3.865 4.250 49GLU O 805 4.144 3.984 4.263 50MET N 806 4.286 3.822 4.199 50MET H 807 4.301 3.722 4.190 50MET CA 808 4.405 3.904 4.182 50MET HA 809 4.377 4.008 4.198 50MET CB 810 4.510 3.865 4.285 50MET HB1 811 4.565 3.777 4.252 50MET HB2 812 4.587 3.940 4.292 50MET CG 813 4.452 3.835 4.423 50MET HG1 814 4.353 3.796 4.425 50MET HG2 815 4.514 3.755 4.462 50MET SD 816 4.453 3.976 4.531 50MET CE 817 4.614 3.925 4.588 50MET HE1 818 4.659 3.996 4.655 50MET HE2 819 4.599 3.831 4.640 50MET HE3 820 4.679 3.909 4.502 50MET C 821 4.467 3.887 4.044 50MET O 822 4.445 3.784 3.981 51PRO N 823 4.549 3.984 4.000 51PRO CA 824 4.626 3.972 3.876 51PRO HA 825 4.553 3.969 3.796 51PRO CB 826 4.711 4.099 3.867 51PRO HB1 827 4.810 4.080 3.908 51PRO HB2 828 4.721 4.135 3.765 51PRO CG 829 4.639 4.199 3.954 51PRO HG1 830 4.708 4.273 3.991 51PRO HG2 831 4.564 4.251 3.895 51PRO CD 832 4.572 4.115 4.061 51PRO HD1 833 4.644 4.098 4.141 51PRO HD2 834 4.483 4.163 4.101 51PRO C 835 4.718 3.850 3.874 51PRO O 836 4.762 3.800 3.978 52SER N 837 4.744 3.801 3.753 52SER H 838 4.711 3.859 3.675 52SER CA 839 4.833 3.689 3.720 52SER HA 840 4.822 3.669 3.614 52SER CB 841 4.978 3.722 3.756 52SER HB1 842 4.988 3.744 3.862 52SER HB2 843 5.041 3.636 3.736 52SER OG 844 5.030 3.825 3.676 52SER HG 845 5.110 3.854 3.717 52SER C 846 4.797 3.559 3.791 52SER O 847 4.884 3.479 3.827 53TYR N 848 4.667 3.537 3.811 53TYR H 849 4.602 3.601 3.770 53TYR CA 850 4.613 3.409 3.852 53TYR HA 851 4.505 3.420 3.851 53TYR CB 852 4.645 3.304 3.741 53TYR HB1 853 4.747 3.275 3.756 53TYR HB2 854 4.589 3.212 3.749 53TYR CG 855 4.643 3.353 3.597 53TYR CD1 856 4.529 3.414 3.540 53TYR HD1 857 4.437 3.421 3.595 53TYR CD2 858 4.764 3.349 3.524 53TYR HD2 859 4.854 3.308 3.568 53TYR CE1 860 4.537 3.471 3.411 53TYR HE1 861 4.452 3.523 3.370 53TYR CE2 862 4.770 3.401 3.394 53TYR HE2 863 4.862 3.395 3.338 53TYR CZ 864 4.656 3.460 3.337 53TYR OH 865 4.662 3.504 3.209 53TYR HH 866 4.747 3.489 3.170 53TYR C 867 4.657 3.374 4.000 53TYR O 868 4.670 3.255 4.028 54ARG N 869 4.682 3.473 4.093 54ARG H 870 4.661 3.565 4.055 54ARG CA 871 4.673 3.444 4.245 54ARG HA 872 4.700 3.339 4.251 54ARG CB 873 4.754 3.510 4.374 54ARG HB1 874 4.855 3.504 4.327 54ARG HB2 875 4.748 3.618 4.351 54ARG CG 876 4.730 3.461 4.557 54ARG HG1 877 4.799 3.379 4.533 54ARG HG2 878 4.812 3.521 4.599 54ARG CD 879 4.604 3.380 4.698 54ARG HD1 880 4.559 3.315 4.625 54ARG HD2 881 4.667 3.298 4.735 54ARG NE 882 4.459 3.405 4.816 54ARG HE 883 4.508 3.338 4.886 54ARG CZ 884 4.385 3.397 4.953 54ARG NH1 885 4.342 3.454 4.851 54ARG HH11 886 4.441 3.411 4.820 54ARG HH12 887 4.246 3.444 4.821 54ARG NH2 888 4.261 3.401 5.023 54ARG HH21 889 4.246 3.370 5.123 54ARG HH22 890 4.176 3.464 5.021 54ARG C 891 4.534 3.490 4.285 54ARG O 892 4.460 3.564 4.222 55GLY N 893 4.517 3.462 4.410 55GLY H 894 4.605 3.428 4.447 55GLY CA 895 4.425 3.510 4.506 55GLY HA1 896 4.471 3.539 4.600 55GLY HA2 897 4.375 3.599 4.478 55GLY C 898 4.336 3.393 4.525 55GLY O 899 4.363 3.279 4.483 56ARG N 900 4.226 3.424 4.591 56ARG H 901 4.219 3.519 4.627 ___ gmx-users mailing list
Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program
From: Ge Sunny [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program Date: Wed, 19 Apr 2006 13:32:14 + To Mark: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? There is another problem. I'm not root. Running from binary pack has an error: error: can't create transaction lock on /var/lib/rpm/__db.000 I have tried creating .rpcmacros and all ./rpm subdirectories under my home directory, then run rpm. The error above still occurs. Sorry. I mean .rpmmacros is created which includes: %_topdir my_home/rpm Then run rpm -ivh fftw3-3.0.1-4.x86_64.rpm. It causes error: can't create transaction lock on /var/lib/rpm/__db.000 because I don't have root permission. Sunny _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ 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 _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ 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] FFTW installation error: cannot compile a simple Fortran program
Ge Sunny wrote: To Florian Haberl: I've also tried installing from fftw-3.0.1.tar.gz. Running ./configure can find g77, but another error appears as config.status: error: cannot find input file: rdft/codelets/hc2r/Makefile.in Sounds like a job for the fftw mailing list. To Mark: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? There is another problem. I'm not root. Running from binary pack has an error: error: can't create transaction lock on /var/lib/rpm/__db.000 I have tried creating .rpcmacros and all ./rpm subdirectories under my home directory, then run rpm. The error above still occurs. Sounds like a job for the rpm mailing list. :-) Neither of these are actually gromacs problems. Best of luck. 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] trjcat -settime option
Thank you so much, Yang Ye.
Masa
From: Yang Ye [EMAIL PROTECTED]
Subject: Re: [gmx-users] trjcat -settime option
Date: Wed, 19 Apr 2006 21:00:59 +0800
I missed this for last mail. The use of gmxcheck is to determine the
welding point. So trjconv -b {start_time} -e {end_time} could be
useful in cases like resuming from crash.
Yang Ye
$,3r}r}r}r}r}r}r}r}(B
yes. you are right in both cases. BTW, I have one suggestion to you,
before trjcat, use gmxcheck to check the time in the trajectory.
Yang Ye
[EMAIL PROTECTED] wrote:
Thanks for quick reply, Yang Ye and David,
But my way of asking seemed not good.
I know what trjcat command is.
It is to concatinate two .trr files.
but when we use trjcat command with -settime option,
the command says as following,
c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.
l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.
I am confused which option I should use, either c or l.
We usually, I think, continue the simulation as
changing confout.gro to conf.gro, using grompp to make
a new .tpr file, and mdrun.
As a result, we have two .trr files.
In this case, when we concatinate two .trr files,
using trjcat command with -settime, we should select c(continue),
right?
On the other hand,
Due to some computer failure, we usually use tpbconv command in order to
continue the simulation as Yang and David said.
In this case, after the simulation, when we concatinate two .trr files,
using trjcat command with -settime, should we select l(last)?
Is this correct?
Sorry for bothering you, but I appreciate you if you answer my question.
Best regards,
Masa
--
Masaomi Hatakeyama
Ph.D Candidate(Knowledge Science, JAIST)
[EMAIL PROTECTED]
http://www.jaist.ac.jp/~m-hatake
From: Yang Ye [EMAIL PROTECTED]
Subject: Re: [gmx-users] trjcat -settime option
Date: Wed, 19 Apr 2006 14:40:09 +0800
Hi,
It seems that you got two questions:
1. concat several trajectory together, use trjcat.
2. use tpbconv.
To use tpbconv, just use the last trajectory you have before the
computer failure. Also, to use tpbconv, you will need edr. I suggest you
to use gmxcheck to check both the trr and edr file to find their common
ending point.
Yang Ye
[EMAIL PROTECTED] wrote:
Hello, again
I'm sorry I had a mistake about my question.
When using tpbconv command to make a new topol.tpr and
continue a simulation due to some computer problems(e.g. power failure),
should I select _l_ option?
When I change confout.gro into conf.gro and continue
a simulation, should I select _c_ option?
Best Regards,
Masa
--
Masaomi Hatakeyama
Ph.D Candidate(Knowledge Science, JAIST)
[EMAIL PROTECTED]
From: [EMAIL PROTECTED]
Subject: [gmx-users] trjcat -settime option
Date: Wed, 19 Apr 2006 12:57:28 +0900 (LDT)
Hi everyone,
I'd like to ask a easy question today.
(I didn't understand the command explanation
because of my poor english skill)
Please teach me the difference c(continue) and l(last)
when using -settime option with trjcat command.
I have several trajectory files and want to conbine them,
but I have two types.
one of them: changing confout.gro into conf.gro and continue the
simulation.
the other: using tpbconv command to make a new topol.tpr due to some
computer problems and continue the simulation.
When using tpbconv command to make a new topol.tpr and
continue a simulation due to some computer problems(e.g. power failure),
should I use -l option?
When I change confout.gro into conf.gro and continue
a simulation, should I use -o option?
If I don't use -settime option, what happen?
Thanks in advance,
Masa
--
Masaomi Hatakeyama
Ph.D Candidate(Knowledge Science, JAIST)
[EMAIL PROTECTED]
___
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[gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux box (suse 10.0) and Gromacs 3.3. Everything is fine until this command: nohup mdrun -s trp_pr.tpr -o trp_pr.trr -c trp_b4md.gro -g pr.log -e pr.edr That ends abnormally with a segmentation fault. I searched the mailing list archive but I didn't find anything helpful. Has anybody tried this tutorial with Gromacs 3.3 (it's tested on 3.2.1)? Any help is greatly appreciated. Zorzan Simone. pr.mdp, mdout.mdp and pr.log follows. pr.mdp title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm =1 nstxout = 250 ; output coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout =0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx=0 fourier_ny=0 fourier_nz=0 pme_order =6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 0.1 tc_grps = proteinsol IN4 Cl ref_t = 300300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 == mdout.mdp == ; ; File 'mdout.mdp' was generated ; By user: simone (1000) ; On host: linux ; At date: Wed Apr 19 16:52:27 2006 ; ; VARIOUS PREPROCESSING OPTIONS title= trp_drg ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 250 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the
[gmx-users] Huge fluctuations for pressure coupling
Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibility = 4.5e-5 tau_p = 1.0 However, I get huge pressure fluctuations (RMS fluctuation of 1.71704e+02) and it seems that the coupling doesn't even enforce the correct pressure (average pressure of 1.68282e-01). I didn't see anyone in the mailing list that had a similar problem. Does anyone know what's going on? Thanks, Bob ___ 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] Huge fluctuations for pressure coupling
Bob Johnson wrote: Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibility = 4.5e-5 tau_p = 1.0 However, I get huge pressure fluctuations (RMS fluctuation of 1.71704e+02) and it seems that the coupling doesn't even enforce the correct pressure (average pressure of 1.68282e-01). I didn't see anyone in the mailing list that had a similar problem. Does anyone know what's going on? Thanks, Bob ___ 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. you fail to specify what length of simulation this is. given the fluctuations the average pressure is spot-on. if you want ten times lower fluctuations you need hundred times more atoms :) -- 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 3.3.1 installation on SGI (Irix): 3
Hi ALL
I got a lot of errors when I did the modifications in the file make_edi.c in
the mnt1.usr/akshayp/src/tools/
Around 101 errors in the same file
I do not understand why all these errors are happening.
Please help me to take care of these errors and install GROMACS 3.3.1 on SGI
Irix.
Looking forward to hear
Regards
Akshay
|-Original Message-
|From: Yang Ye [mailto:[EMAIL PROTECTED]
|Sent: Tuesday, April 18, 2006 7:50 PM
|To: [EMAIL PROTECTED]; Discussion list for GROMACS users
|Subject: Re: [gmx-users] GROMACS 3.3.1 installation on SGI (Irix): 3
|
|You may replace line 579 as
|
|evStepOptions[evLINFIX] = evStepOptions[0]
|
|line 581 as
|
|evStepOptions[evLINACC] = evStepOptions[1]
|
|line 583 as
|
|evStepOptions[evRADFIX] = evStepOptions[2]
|
|Just a quick fix.
|
|Yang Ye
|
|Akshay Patny wrote:
| Hi
|
| As suggested I removed one of the semicolons before the double semicolon
|in
| one of the lines in the file gmx_chi.c
|
| I re-installed again and this time it gave me the following error. Can
|you
| suggest what is going wrong and how can I fix it now?
|
|___
|_
| cc-1028 cc: ERROR File = make_edi.c, Line = 579
| The expression used must have a constant value.
|
| { evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]},
| ^
|
| cc-1028 cc: ERROR File = make_edi.c, Line = 581
| The expression used must have a constant value.
|
| { evStepOptions[evLINACC], FALSE, etSTR, {evParams[evLINACC]},
| ^
|
| cc-1028 cc: ERROR File = make_edi.c, Line = 583
| The expression used must have a constant value.
|
| { evStepOptions[evRADFIX], FALSE, etREAL, {radfix},
| ^
|
| cc-1552 cc: WARNING File = make_edi.c, Line = 622
| The variable bTop is set but never used.
|
| bool bTop, bM, bFit1;
|^
|
| 3 errors detected in the compilation of make_edi.c.
| *** Error code 2 (bu21)
| *** Error code 1 (bu21)
| *** Error code 1 (bu21)
|
|___
|_
|
| I really appreciate your help.
|
| Kind Regards
| Akshay
|
| Akshay Patny
|
|
| Graduate Research Assistant
| Faser Hall 417, Department of Medicinal Chemistry
| Research Institute of Pharmaceutical Sciences
| University of Mississippi
| University, MS 38677
| E-mail: [EMAIL PROTECTED]
| Tel: 662-915-1286 (office); Web: www.olemiss.edu
|
| |-Original Message-
| |From: David van der Spoel [mailto:[EMAIL PROTECTED]
| |Sent: Tuesday, April 18, 2006 12:22 AM
| |To: [EMAIL PROTECTED]; Discussion list for GROMACS users
| |Subject: Re: [gmx-users] GROMACS 3.3.1 installation on SGI (Irix): 2
| |
| |Akshay Patny wrote:
| | Hi
| | Hi ALl
| |
| | I read through some of the e-mails of B. Nataraj and Erik Lindahl for
| | similar problem on compiling of GROMACS 3.3.1 on SGI IRIX.
| |
| | As my error also pointed to a problem in gmx_fft_fftw3.c, I replaced
| |the
| | 'void' with 'char' in the line 150 of the file, as suggested.
| |
| | I got the errors exactly the same as B. Nataraj got after doing this
| | modification, which is listed at
| | http://www.gromacs.org/pipermail/gmx-users/2006-April/020969.html
| |
| | The same error is given below. I could not understand how to fix this
| |error
| | and run GROMACS successfully.
| |
| | Dr. Erik Lindahl wrote that: As far as I can see that file is
|perfectly
| | valid ANSI C - there is no executable statement in the declaration
| |section.
| |
| | However, I still do not know how to fix this?
| |
| |
| |there is a double semicolon on one of the lines before it. please remove
| |it and retry.
| |
| | Please help.
| |
| | Regards
| | Akshay
| |
| | Error is given below:
| |
|
||__
|_
| |_
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1031
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | static real core_frac=0.5 ;
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1032
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | t_pargs pa[] = {
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1073
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | FILE *log;
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1074
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | intnatoms,nlist,naa,idum,nbin;
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1075
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | t_atomsatoms;
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1076
| | A declaration cannot appear after an executable statement in a
|block.
| |
| | rvec *x;
| | ^
| |
| | cc-1241 cc: ERROR File = gmx_chi.c, Line = 1077
| | A declaration cannot appear after an executable
Re: [gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting pme_order = 4 is a workaround in case you don't want to upgrade to 3.3.1. --Tom On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote: Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux box (suse 10.0) and Gromacs 3.3. Everything is fine until this command: nohup mdrun -s trp_pr.tpr -o trp_pr.trr -c trp_b4md.gro -g pr.log - e pr.edr That ends abnormally with a segmentation fault. I searched the mailing list archive but I didn't find anything helpful. Has anybody tried this tutorial with Gromacs 3.3 (it's tested on 3.2.1)? Any help is greatly appreciated. Zorzan Simone. pr.mdp, mdout.mdp and pr.log follows. pr.mdp title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm =1 nstxout = 250 ; output coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout =0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx=0 fourier_ny=0 fourier_nz=0 pme_order =6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 0.1 tc_grps = proteinsol IN4 Cl ref_t = 300300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 == mdout.mdp == ; ; File 'mdout.mdp' was generated ; By user: simone (1000) ; On host: linux ; At date: Wed Apr 19 16:52:27 2006 ; ; VARIOUS PREPROCESSING OPTIONS title= trp_drg ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 250 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ;
[gmx-users] g_sdf for Gromacs 3.3 or any other tool for Spatial Distributions .
Dear all, Does anybody have the g_sdf ported for GROMACS 3.3 ? The g_sdf is a program for calculations of Spatial Distribution Functions (SDFs). It is not from the official distribution - it is written by Christoph Freudenberger whom I am not able to find (his old e-mail is expired). I've got the code from Dallas Warren (thanks, Dallas!) - but it uses an old version of pbc_dx function with 3 input parameters (now the pbc_dx uses 4 input parameters). I wouldn't mind to recompile this program with an old version of Gromacs - but I am going to analyse plenty of trajectories and topologies obtained with 3.3. version. So, I afraid of possible incompatibilities, bugs etc. There is always another option - correct the code by myself, but ... May be somebody has already ported the g_sdf for 3.3 or has another tool for calculations of SDFs? With kindest regards, Maxim. Maxim V. Fedorov ___ 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] OPLS modification between 3.3 and 3.3.1??
Hello, ffoplsaa.rtp has changed in the 3.3.1 release. However, there are no references given and no special notification of this fact. I was wondering if anybody knows the references for this change. Here is the difference between the two distributions: diff ~/TEST/gromacs-3.3/share/top/ffoplsaa.rtp ~/TEST/gromacs-3.3.1/share/top/ffoplsaa.rtp 1008,1010c1008,1010 CDCENZ HZ1dih_LYSH_chi5_C_C_N_H CDCENZ HZ2dih_LYSH_chi5_C_C_N_H CDCENZ HZ3dih_LYSH_chi5_C_C_N_H --- CDCENZ HZ1dih_LYS_chi5_C_C_N_H CDCENZ HZ2dih_LYS_chi5_C_C_N_H CDCENZ HZ3dih_LYS_chi5_C_C_N_H 1025c1025 CGopls_2100.09753 --- CGopls_2100.048 3 1028,1029c1028,1029 SDopls_202 -0.435 4 CEopls_2090.03755 --- SDopls_202 -0.335 4 CEopls_209 -0.013 5 1325,1326c1325,1326 NCACBCGdih_GLU_chi1_N_C_C_C CGCBCA Cdih_GLU_chi1_C_C_C_CO --- NCACBCGdih_TRP_chi1_N_C_C_C CGCBCA Cdih_TRP_chi1_C_C_C_CO ___ 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] Please Help: Still facing problems with installing Gromacs 3.3.1 on SGI Irix
SUBJECT: Still facing problems with installing
Gromacs 3.3.1 on SGI Irix
Hi
As suggested by Dr. Spoel, I removed one of the
semicolons before the double semicolon in one of the lines in the file
gmx_chi.c
I re-installed again and this time it gave me the
following error. Can you suggest what is going wrong and how can I fix it now?
cc-1028 cc: ERROR File = make_edi.c, Line = 579
The _expression_ used must have a constant
value.
{
evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 581
The _expression_ used must have a constant
value.
{
evStepOptions[evLINACC], FALSE, etSTR, {evParams[evLINACC]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 583
The _expression_ used must have a constant
value.
{
evStepOptions[evRADFIX], FALSE, etREAL, {radfix},
^
cc-1552 cc: WARNING File = make_edi.c, Line = 622
The variable bTop is set but
never used.
bool bTop, bM, bFit1;
^
3 errors detected in the compilation of
make_edi.c.
*** Error code 2 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
I really appreciate your help.
Kind Regards
Akshay
Akshay Patny
Akshay Patny
Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical
Sciences
University
of Mississippi
University,
MS 38677
E-mail: [EMAIL PROTECTED]
Tel: 662-915-1286 (office);
Web: www.olemiss.edu
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[gmx-users] LINCS Warning with MDRUN - Segmentation Fault
HiAttached is part of the gro file which gave the LINCS error on atoms. Thisoutput is the gro file for the initial mdrun, after which final grompp andfinal mdrun was done, which gives the error I described in the message below.Gaurav Gaurav Chopra wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. you need to minimize better, but if your structures are really bad it won't help either (e.g. when you have a sidechain sticking through a ring) -- 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 spoel at xray.bmc.uu.sespoel at gromacs.orghttp://folding.bmc.uu.se The lincs warnning are on water molecules isn't it ??? XAvier Output set 710 with rmsf= 1.614 of 1dsl.cl_nH_tir.pdb in water49GLUHB2 797 4.183 3.686 4.460 49GLU CG 798 4.026 3.813 4.538 49GLUHG1 799 4.042 3.915 4.502 49GLUHG2 800 3.919 3.800 4.550 49GLU CD 801 4.094 3.805 4.672 49GLUOE1 802 4.149 3.697 4.707 49GLUOE2 803 4.086 3.910 4.737 49GLU C 804 4.170 3.865 4.250 49GLU O 805 4.144 3.984 4.263 50MET N 806 4.286 3.822 4.199 50MET H 807 4.301 3.722 4.190 50MET CA 808 4.405 3.904 4.182 50MET HA 809 4.377 4.008 4.198 50MET CB 810 4.510 3.865 4.285 50METHB1 811 4.565 3.777 4.252 50METHB2 812 4.587 3.940 4.292 50MET CG 813 4.452 3.835 4.423 50METHG1 814 4.353 3.796 4.425 50METHG2 815 4.514 3.755 4.462 50MET SD 816 4.453 3.976 4.531 50MET CE 817 4.614 3.925 4.588 50METHE1 818 4.659 3.996 4.655 50METHE2 819 4.599 3.831 4.640 50METHE3 820 4.679 3.909 4.502 50MET C 821 4.467 3.887 4.044 50MET O 822 4.445 3.784 3.981 51PRO N 823 4.549 3.984 4.000 51PRO CA 824 4.626 3.972 3.876 51PRO HA 825 4.553 3.969 3.796 51PRO CB 826 4.711 4.099 3.867 51PROHB1 827 4.810 4.080 3.908 51PROHB2 828 4.721 4.135 3.765 51PRO CG 829 4.639 4.199 3.954 51PROHG1 830 4.708 4.273 3.991 51PROHG2 831 4.564 4.251 3.895 51PRO CD 832 4.572 4.115 4.061 51PROHD1 833 4.644 4.098 4.141 51PROHD2 834 4.483 4.163 4.101 51PRO C 835 4.718 3.850 3.874 51PRO O 836 4.762 3.800 3.978 52SER N 837 4.744 3.801 3.753 52SER H 838 4.711 3.859 3.675 52SER CA 839 4.833 3.689 3.720 52SER HA 840 4.822 3.669 3.614 52SER CB 841 4.978 3.722 3.756 52SERHB1 842 4.988 3.744 3.862 52SERHB2 843 5.041 3.636 3.736 52SER OG 844 5.030 3.825 3.676 52SER HG 845 5.110 3.854 3.717 52SER C 846 4.797 3.559 3.791 52SER O 847 4.884 3.479 3.827 53TYR N 848 4.667 3.537 3.811 53TYR H 849 4.602 3.601 3.770 53TYR CA 850 4.613 3.409 3.852 53TYR HA 851 4.505 3.420 3.851 53TYR CB 852 4.645 3.304 3.741 53TYRHB1 853 4.747 3.275 3.756 53TYRHB2 854 4.589 3.212 3.749 53TYR CG 855 4.643 3.353 3.597 53TYRCD1 856 4.529 3.414 3.540 53TYRHD1 857 4.437 3.421 3.595 53TYRCD2 858 4.764 3.349 3.524 53TYRHD2 859 4.854 3.308 3.568 53TYRCE1 860 4.537 3.471 3.411 53TYRHE1 861 4.452 3.523 3.370 53TYRCE2 862 4.770 3.401 3.394 53TYRHE2 863 4.862 3.395 3.338 53TYR CZ 864 4.656 3.460 3.337 53TYR OH 865 4.662 3.504 3.209 53TYR HH 866 4.747 3.489 3.170 53TYR C 867 4.657 3.374 4.000 53TYR O 868 4.670 3.255 4.028 54ARG N 869 4.682 3.473 4.093 54ARG H 870 4.661 3.565 4.055 54ARG CA 871 4.673 3.444 4.245 54ARG HA 872 4.700 3.339 4.251 54ARG CB 873 4.754 3.510 4.374 54ARG
Re: [gmx-users] Installation Error on an Athlon64 with Intel Compiler
Jones de Andrade wrote: Hi all! I'm trying to compile gromacs 3.3.1 on an Athlon64 (core venice) with the intel compiler (icc version 9.0.030). I've tried a lot of flags, and also no flags. All times I get the following error, after which everything fails: It is not related to FLAGS. /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_innerloop.o mknb_innerloop.c mknb_innerloop.c(362): warning #188: enumerated type mixed with another type mknb_func.coul=coulsave; ^ mknb_innerloop.c(363): warning #188: enumerated type mixed with another type mknb_func.vdw=vdwsave; ^ These warnings are common with icc, which claims to be a more standard compiler. /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -c -o mknb_interactions.o mknb_interactions.c /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -o mknb mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o mknb_outerloop.o mknb_innerloop.o mknb_interactions.o rm -f kernel-stamp ./mknb -software_invsqrt Would like to go to /home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel and run this command. ./mknb -software_invsqrt This program has some problem to run. I suspect that you are using a 32-bit ICC in conjunction with 64-bit system library. Gromacs nonbonded kernel generator (-h for help) Generating single precision functions in C. Using Gromacs software version of 1/sqrt(x). make[5]: *** [kernel-stamp] Falha de segmentação make[5]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel' make[4]: ** [all-recursive] Erro 1 . . . Does anybody got such an error before? The program compiled well within gcc and pgi compilers. Thanks in advance for everything! :D Jones ___ 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 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] Unnatural amino acid problems
Hello I am parametrizing an unnatural amino acid, phenylglycine (PHG), in the OPLS FF in GROMACS. I have put in the necessary parameters in the .hdb, .rtp, and the aminoacids.dat file. 1. When I do grompp for the EM, I get an error saying that I have not put in the appropriate parameters for the bonds, angles and dihedrals. Surprisingly, when I do put in the parameters (from the ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more distorted, a counterintuitive observation. In fact the simulation is much better off when I ignore the warnings and the program puts in zeros after the required parameters in the .top file. Why is this happening? Another question related to this: 2. When I do parametrize a single peptide with a single PHG residue and then simulate it (with zeros for the parameters in the .top file), the PHG turns out fine and does not get distorted. But when I simulate many PHG containing peptides, say 10 of them stacked on top of and besides each other, I observe that some of the PHGs get distorted while others don't. By distorted, I especially mean the Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from its normal value of about 109. Whatever the cause for this distortion is, why is it affecting only some PHG residues and not others? Thank you Regards, Ashutosh Jogalekar Emory University. ___ 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] Unnatural amino acid problems
Hello I am parametrizing an unnatural amino acid, phenylglycine (PHG), in the OPLS FF in GROMACS. I have put in the necessary parameters in the .hdb, .rtp, and the aminoacids.dat file. 1. When I do grompp for the EM, I get an error saying that I have not put in the appropriate parameters for the bonds, angles and dihedrals. Well that means you haven't done it :-) Go back and compare what you've done for PHG with other amino acids, see what is different and fix it. Surprisingly, when I do put in the parameters (from the ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more distorted, a counterintuitive observation. In fact the simulation is much better off when I ignore the warnings and the program puts in zeros after the required parameters in the .top file. Why is this happening? You can't tell that your force field is a reasonable physical model by looking at the results on their own - you need a comparison with experiment. Often you can tell by looking at the results that it is completely wrong, however. Just putting in zeroes guarantees you a spurious model, whether you can recognise that from the results or not. Another question related to this: 2. When I do parametrize a single peptide with a single PHG residue and then simulate it (with zeros for the parameters in the .top file), the PHG turns out fine and does not get distorted. But when I simulate many PHG containing peptides, say 10 of them stacked on top of and besides each other, I observe that some of the PHGs get distorted while others don't. By distorted, I especially mean the Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from its normal value of about 109. Whatever the cause for this distortion is, why is it affecting only some PHG residues and not others? It's a stochastic system... run it for long enough and you'll see weird stuff everywhere. 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
