Re: [gmx-users] intel compiler + amd64: help needed.
Are you using the ICC with EM64T extension? I would like you to look at the nature of the program: GROMACS code is unique as comparing to other computational software: its core code is written in assembly code which simply can not be optimized further by the compiler. What can be optimized is just the procedure calling time and the outer-loop code which accounts for little computational time (As there is no complete study, but a few benchmarking runs which fluctuate 5% is considered as same for programs). CPMD and other software is another story which you have the free lunch of the compiler. Yang Ye Jones de Andrade wrote: Hi all. First of all, thanks everybody for the help. ;) Yang, I know, I know. I should keep to the GNU. But lets say that I get addicted to the intel compiler on a cpmd winter school, when it appeared in front of me as the only freely available for both amd and intel cpus fortran90 compiler. Since it also came with performance for free, that was a good deal. I also have just a handfull of tuning flags I use for icc and ifort. But, like everybody in here, we choose the machines for performance (which means, first corret result, and later speed), same goes for me for the compilers. Moreover, as I said before: I wana try QM/MM, and CPMD doesn't work with gcc. Back to the subject: David, thanks for the piece of gmx4 code. Unfortunatelly, it don't work. I deleted all the objects from the directory before trying to compile to assure that, and it yelded the same error. On the other hand, the trick of compiling just mknb in gcc, and the rest with icc got a bit farther, before crashing... but still gone with about a thousand of weird warnings. I'm sending the window desktop outputs attached in this message. Anyway, in order to make that trick, I've used the following script: export CPPFLAGS=-I/usr/local/lib64/fftw/gnu/include export LDFLAGS=-L/usr/local/lib64/fftw/gnu/lib export CC=/usr/local/bin/gcc export CFLAGS=-O3 -ffast-math -funroll-all-loops -fpeel-loops make distclean ./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3 cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.gcc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.gcc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.gcc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.gcc export PATH=$PATH /usr/local/intel/bin/ . /usr/local/intel/lib/ export LD_LIBRARY_PATH=/usr/local/intel/lib/ export CPPFLAGS=-I/usr/local/lib64/fftw/intel/include export LDFLAGS=-L/usr/local/lib64/fftw/intel/lib export CC=/usr/local/intel/bin/icc export CXX=/usr/local/intel/bin/icpc export F77=/usr/local/intel/bin/ifort export CFLAGS= export CXXFLAGS= export FFLAGS= export CFLAGS=-O3 -axP -xW -ipo -static export CXXFLAGS=-O3 -axP -xW -ipo -static export FFLAGS=-O3 -axP -xW -ipo -static make distclean ./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3 --disable-x86-64-sse cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.icc cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.icc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.icc cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.icc cp ./Makefile.mknb.gcc ./src/gmxlib/nonbonded/nb_kernel/Makefile cp ./Makefile.mknb_kernel_ia32_3dnow.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile cp ./Makefile.mknb_kernel_ia32_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile cp ./Makefile.mknb_kernel_ia32_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile cp ./Makefile.mknb_kernel_x86_64_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile cp ./Makefile.mknb_kernel_x86_64_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile make The output from it isn't attached. :( Sorry, The gziped file is too big for the list limits. Anyway, despite lots of warnings, the compilations ends dieing in here: * /tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function' /tmp/ipo_iccpmJSXr.o(.text+0x2edde):/tmp/ipo_iccpmJSXr.c: undefined reference to
Re: [gmx-users] intel compiler + amd64: help needed.
Hi Jones,There are two things I can think of immediately:1. Make sure to set optimization and architecture options for portable code. By default, the intel compiler might generate binaries that use SSE3-specific stuff, although it is unlikely in this part of the code.2. Try setting "CC_FOR_BUILD=gcc" before running configure, or as an argument when calling make. This will use a different compiler for code that is executed during the build process (important for cross-compiling, and on systems where you cannot execute mpicc-compiled programs outside the queue).Cheers,Erik Program received signal SIGSEGV, Segmentation fault. 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6 (gdb) where #0 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6 #1 0x2b140e6f in vfprintf () from /lib64/tls/libc.so.6 #2 0x2b15e2a9 in vsprintf () from /lib64/tls/libc.so.6 #3 0x2b149568 in sprintf () from /lib64/tls/libc.so.6 #4 0x0040248b in mknb_code (format=0x40cd2e "s") at mknb_metacode.c:282 #5 0x00401aaf in mknb_declare_real (name=0x7fffd0d0 "ix1,iy1,iz1,fix1,fiy1,fiz1") at mknb_metacode.c:104 #6 0x00403e62 in mknb_declare_variables () at mknb_declarations.c:258 #7 0x00400fef in mknb_write_function () at mknb.c:154 #8 0x004017cf in main (argc=1, argv=0x7fffd628) at mknb.c:348 Well, what does this kind of stuff means? It worries about the libc 4 times, but also about the other files. :( What shall I look at? David Mathog: thanks also. But, how could I fix that? Thanks a lot for everything. JonesOn 5/31/06, David van der Spoel [EMAIL PROTECTED] wrote: gdb whereit will tell you the line in the mknb this was called from.if you call a library function with garbage data it may crash there...--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 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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] Buckingham instead of LJ.
karamyog singh wrote: Is it not possible to use Buckingham potential instead of default LJ potential for interaction between same atoms? Read the manual. Section 4.1 would be a good start. 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] Position restrain
While running a MD of PE with position restrain, i get this error message Fatal error: [ file posre.itp, line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your molecule only has 12 atoms and by the way, the error message is from grompp. actually my molecule has 12 thousand atoms, half of it dummies and half AUA. The .gro and .ndx contains atoms numbered up to 12000 The error ideed comes from grompp. Thanx Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden winmail.dat___ 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] Buckingham instead of LJ.
karamyog singh wrote: I request you to see section 5.3.3 . Under the [ atomtypes ] section displayed over there I want to replace c6 and c12 by buckingham potential. I want to replace O-O LJ interaction with O-O Buckingham interaction. Just below that the manual shows [ nonbond_params ] where I think I can change the function type from 1 to 2 to use Buckingham potential. However that does not seem to work as the software takes LJ interaction parameters from the [ atomtypes ] section itself. I got no change in my results when I did that. Any idea as to what can be wrong? your topology I'm afraid. Please read manual more carefully. You'll have to supply correct buckingham parameters. - Karamyog. On 6/1/06, *Mark Abraham* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: karamyog singh wrote: Is it not possible to use Buckingham potential instead of default LJ potential for interaction between same atoms? Read the manual. Section 4.1 would be a good start. Mark ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] mailto:[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 -- 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] Position restrain
Hi,
concept of 'molecules' as it is applied within Gromacs has been discussed
several times already, also with regards to distance restraints, which can
not be defined between different 'molecules'. Of course you can define
distance restraints between 'real' molecules by having the molecules
within the same topology block (atoms,bonds etc.), just without any
bonding parameters defined between them. Position restraints also have
to be defined for each topology block ('molecule') and are read in this
way by grompp. The index file .ndx referres to the atom numbering in the
structure file (.pdb .gro ...). The id's of the position restraints,
however,
refer to atom numbering within the 'molecule', starting from 1 for each, and
thus ,must be defined/included right after the corresponding 'molecule'
in the
.top file.
This is a little confusing and my chaotic description might not help a lot,
but it seems you have more than one 'molecule' in your system and the
one you want the position restraints for only has 12 atoms, even though it
might have the atom id 101 in your coordinate file.
Best regards,
Uwe
Alessandro Mattozzi wrote:
While running a MD of PE with position restrain, i get this error message
Fatal error: [ file posre.itp, line 6 ]:
Atom index (101) in position_restraints out of bounds (1-12)
My atom index goes up to 6000, why do I have to be in the 1-12 range?
your molecule only has 12 atoms and by the way, the error message is
from grompp.
actually my molecule has 12 thousand atoms, half of it dummies and half AUA.
The .gro and .ndx contains atoms numbered up to 12000
The error ideed comes from grompp.
Thanx
Regards
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
___
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] freeenergy calculation
i have completed my simulation.i want to analyse my protein.can u help me how to calculate the free binding energy calculation,which program i should use.i've read gromacs manual 3.3 but i'm in need of any other new analysis are included in version 3.3 or not.so where can i getthe information on availability of more analysis in GROMACS 3.3 version comapred to older version. thanks sir.i'm in hurry.Plz anyone help me. _ Fall in Love... Get married! Join FREE! http://www.shaadi.com/ptnr.php?ptnr=msnhottag ___ 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] do_dssp with no output!
I have the same problem. Any suggestion??? DSSP variable is setup correctly, but nothing happens when I run do_dssp. It just freeze as Elena described. Thanks in advance, César.- ___ 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] enabling threads in GROMACS
hi all IS it possible to enable threads in gromacs during configuration? Thanks Jayant Jayasundar JayantJames Postdoc, Department ofVeterinary andComparative Anatomy,Pharmacology andPhysiology(VCAPP), Washingtonstate university,Pullman 99164-6520,USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937,Cell:1-509-432-5790 ___ 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] enabling threads in GROMACS
Jayant James Jayasundar wrote: hi all IS it possible to enable threads in gromacs during configuration? Thanks Jayant no, and it won't help in anyway because nothing has been implemented in 3.3 yet. Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/[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 -- 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] Problems Looking at Graphic Output
DearGROMACS community, I am new to Linux and GROMACS. I successfully installed Gromacs on TopologiLinux. I can run the examples in tutorial folder without problems, butI can't look on anygraphic output because I don't have "xmgrace" installed. I did some Internet searches and was able to findand download its decendant - Grace.However, I was unable to install it because Grace can't findthe Motif libraries. After looking into my system I was able to find "lesstif" folder in /usr/doc/ (LessTif is suposed to bea replacement forMotif, as far as I understand from reading LessTif and Grace web-pages), but I am still not sure if it is installed onmy system (is there any way to find this out? how can I get Grace to find and use LessTif libraries? path to which fileshould Idefine for ./configure to find them?). Aftersome moreInternet searching I foundand downloaded OpenMotif. Unfortunately, I was unable to install it due tomany errors. I am not sure what to do now (I very much would like to be able to look at graphic outputs) and any help will be appreciated. Natalia. P.S. Do I need to reinstall GROMACS once I install Grace?___ 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] Problems Looking at Graphic Output
Zakharova, Natalia Leonidovna wrote: Dear GROMACS community, I am new to Linux and GROMACS. I successfully installed Gromacs on TopologiLinux. I can run the examples in tutorial folder without problems, but I can't look on any graphic output because I don't have xmgrace installed. I did some Internet searches and was able to find and download its decendant - Grace. However, I was unable to install it because Grace can't find the Motif libraries. After looking into my system I was able to find lesstif folder in /usr/doc/ (LessTif is suposed to be a replacement for Motif, as far as I understand from reading LessTif and Grace web-pages), but I am still not sure if it is installed on my system (is there any way to find this out? how can I get Grace to find and use LessTif libraries? path to which file should I define for ./configure to find them?). After some more Internet searching I found and downloaded OpenMotif. Unfortunately, I was unable to install it due to many errors. I am not sure what to do now (I very much would like to be able to look at graphic outputs) and any help will be appreciated. Natalia. P.S. Do I need to reinstall GROMACS once I install Grace? no. your lnux distribution probably has an easy way to install either lesstif or openmotif. Check the website for the linux distro. ___ 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 -- 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] How do I redirect grompp errors to a file for parsing?
David Mobley wrote: So, this is probably a stupid question, but for some reason I can't figure out how to do it... I need to run a ton of small MD jobs for a whole bunch of different small molecules, some few of which have errors in their topologies which cause grompp to fail with an error. Therefore, I need some automated way of grabbing the output of grompp and parsing it to identify errors so that I can go back and track down the problems. However, I can't for the life of me figure out how to get grompp to do anything other than just print the errors to the screen. For example, standard things like: grompp (usual args) file.dat at least for csh for sh it is more like 21 man csh man bash fail to redirect the errors. Any suggestions? I'm sure I'm missing something obvious. Thanks, David ___ 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 -- 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] Problems Looking at Graphic Output
Try installing VMD, this software is nice to inspect molecular dynamics results with gromacs. Good luck Cesar Zakharova, Natalia Leonidovna escribió: Dear GROMACS community, I am new to Linux and GROMACS. I successfully installed Gromacs on TopologiLinux. I can run the examples in tutorial folder without problems, but I can't look on any graphic output because I don't have xmgrace installed. I did some Internet searches and was able to find and download its decendant - Grace. However, I was unable to install it because Grace can't find the Motif libraries. After looking into my system I was able to find lesstif folder in /usr/doc/ (LessTif is suposed to be a replacement for Motif, as far as I understand from reading LessTif and Grace web-pages), but I am still not sure if it is installed on my system (is there any way to find this out? how can I get Grace to find and use LessTif libraries? path to which file should I define for ./configure to find them?). After some more Internet searching I found and downloaded OpenMotif. Unfortunately, I was unable to install it due to many errors. I am not sure what to do now (I very much would like to be able to look at graphic outputs) and any help will be appreciated. Natalia. P.S. D o I need to reinstall GROMACS once I install Grace? ___ 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] Problems Looking at Graphic Output
Hi Natalia, Download Xmgrace from this place and install the rpm. http://rpmfind.net/linux/RPM/suse/9.0/i386/suse/i586/ xmgrace-5.1.12-112.i586.html While installing the rpm if you get an error, further Scrolling down the page u will see links to the requirements for this to install...from where you can download the dependencies (also in rpm) and finish install. Hope this helps Venks Venky Krishnamani Dr.Janos K. Lanyi Lab, D320, Medical Sciences D University of California, Irvine On Jun 1, 2006, at 11:54 AM, cesar wrote: Try installing VMD, this software is nice to inspect molecular dynamics results with gromacs. Good luck Cesar Zakharova, Natalia Leonidovna escribió: Dear GROMACS community, I am new to Linux and GROMACS. I successfully installed Gromacs on TopologiLinux. I can run the examples in tutorial folder without problems, but I can't look on any graphic output because I don't have xmgrace installed. I did some Internet searches and was able to find and download its decendant - Grace. However, I was unable to install it because Grace can't find the Motif libraries. After looking into my system I was able to find lesstif folder in /usr/doc/ (LessTif is suposed to be a replacement for Motif, as far as I understand from reading LessTif and Grace web-pages), but I am still not sure if it is installed on my system (is there any way to find this out? how can I get Grace to find and use LessTif libraries? path to which file should I define for ./configure to find them?). After some more Internet searching I found and downloaded OpenMotif. Unfortunately, I was unable to install it due to many errors. I am not sure what to do now (I very much would like to be able to look at graphic outputs) and any help will be appreciated. Natalia. P.S. D o I need to reinstall GROMACS once I install Grace? - --- ___ 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] Steered Molecular Dynamics in GROMACS
Hello, Can anyone describe the general procedure for SMD in GROMACS? (i.e. how you designate which atoms are to be pulled, in what direction, and by what force). Thanks, Arneh ___ 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] Paralell problems...
Dear GRMxers: We need some help in running our Gromacs 3.2.1 parallel environment in 5 nodes of SunFires V20v (dual-core Opteron 2.2, 4 GB DDR2 RAM), gigabit eth, mpich-1.2.7, using Sun Grid Engine 6.0. In a 2 processors job (single node), the results are O.K. but in a 4, 6 or 8 processors (2, 3 or 4 nodes) in the machine log files we have: In #8220; -np 4#8221; the error was : p4_5991: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: p4_error: net_recv read: probable EOF on socket: 1 p5_5996: p4_error: Timeout in establishing connection to remote process: 0 p0_8456: (333.761719) net_send: could not write to fd=4, errno = 32 In #8220; #8211;np 8#8221; the error was: p0_16398: p4_error: interrupt SIGSEGV: 11 In all the cases, we obtain a #8220;Killed by signal 2#8221; at the end of the gromacs log, and process stopped. Grompp was executed with the -np option, and our final script was: #$ -v MPIRUN #$ -v MPICH_PROCESS_GROUP MPIRUN -np $NSLOTS -machinefile $TMPDIR/machinefile /nfs/gromacs-3.2. 1_paralelo/x86_64-unknown-linux-gnu/bin/mdrun -np 6 -s ABint/ABint_md.tpr -o ABint/ABint_md.trr -c ABint/ABint_md.gro -e ABint/ABintener.edr -g ABint/ ABintmd.log -nice 0 Any help will be extremely appreciated: Jorge H.F. -- == Dr. JORGE HERNANDEZ FERNANDEZ == == Center of Applied Toxinology == = CAT-CEPID - Instituto Butantan = == Ave Vital Brasil, 1500 S.P. == Tel: 055 11 3726 7222 r.2042 Fax: 055 11 3721 6605 S.B.I.- EMBRAPA - BioInformatica C.p. 6041 Cidade Universitária Zeferino Vaz = Barão Geraldo Campinas S.P. === 13080-970 Tel: 055 19-37895828 Cell: 055 11-97126104 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] intel compiler + amd64: help needed.
Hi all!. First, sorry for the delay in getting in touch again. Bureaucracy. :P Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :) Anyway, here is where I'm now: Erik: I'm sure about the flags. Not using the ones for SSE3, despite my processor having those. I'll just try to activate those as soon as I get a compiling procedure. By now, I even using the --disable-x86-64-sse flag for configure, just to be sure. ;) Also, I tried the CC_FOR_BUILD=gcc environment, but despite it has gone throw the invsqrt compilation, I looked in and it was compiling everything with gcc, and nothing with icc. :( Yang: Yes, I'm using the intel compiler with emt64. I reinstalled the software step by step specifically to be sure about this point. And I understand that gromacs has an assembly core, and that this is basically the heart of the program speed. But, even thow, 5-10% means something, and every nano-second counts. Specially when you have a big delay to deal with, and that this 10% mean 0.25ns. ;) Even then, after I successfully compile it we will be able to say for sure how much if extra performance (if it yelds any) does the intel compiler gives on AMD64 machines. Moreover, as I said in a long time ago message: I want to use QM/MM with gromacs+cpmd, and at this point I really dislike the idea of compiling one thing with intel (cpmd) and the other with gcc (gromacs). Since I can't make cpmd work on gcc, I'm trying to make gromacs work on intel. ;) David (last but not the least): I removed the -ipo flag from the compilations. Also, I've added --without-motif-libraries --without-motif-includes --without-x flags to the configure script. On the other hand, I've been greping a bit the directories for the invsqrt calls My God, it's not the heart of the program, it's the sinapses among its neurones. Am I wrong, or there is about some thousands of those calls to be changed? Is it right? If it is, just let me know, cause I'm tracking those down (finding a script way to back up original files before edition.) and at the same time trying to find some sort of magical flag to convince icc to *not* use the invsqrt function or the math.h file at all (second choice seems to me a bit too strong). Seems that if it can be done on a flag it will be really helpfull (and easier) for most of the users. The good new is that there is no other error message in the ompilation, as I can see (And just a few warnings to see later, since they look more or less pointless). By the way, can I ask you what was the mknb program for, anyway? :) Again, thanks a lot to everybody in advance, for all the help an advices provided up to now! If I manage to finish this one, I promisse to post those extra benchmarks too, as well as a tutorial on how to compile gromacs on AMD64 machines with non-sense copilers. ;) JonesOn 6/1/06, David van der Spoel [EMAIL PROTECTED] wrote: make[3]: ** [grompp] Erro 1 make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/kernel' make[2]: ** [all-recursive] Erro 1 make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs- 3.3/src' make[1]: ** [all] Erro 2 make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src' make: ** [all-recursive] Erro 1 ** Trying withou the -ipo flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with double invsqrt(double) (declared at line 565 of /usr/local/intel/include/math.h) rename all gromacs invsqrt calls to gmx_invsqrtbe assured that invsqrt didn't exist in the intel compiler in previousreleases, but now that it does we'll have to adapt it seems.ipo is useless for gromacs. do also turn off X11 at the configure stage--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 ___ 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] intel compiler + amd64: help needed.
Hi all. On 6/1/06, David van der Spoel [EMAIL PROTECTED] wrote: Trying withou the -ipo flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with double invsqrt(double) (declared at line 565 of /usr/local/intel/include/math.h)rename all gromacs invsqrt calls to gmx_invsqrt Just a stupid question. No, unfortunatelly I still didn't found a magic flag (trying to be in touch with the intel premier support still). Anyway, I was trying to grep every invsqrt in gromacs directories, and after verbosing out strings like invsqrta, _invsqrt, invsqrtdata, vecinvsqrt, invsqrtm, invsqrtfracttab and invsqrtexptab, and also some comments stuff... Well, the command line below: grep -Hni 'invsqrt' -r * | grep -v 'Arquivo' | grep -v '#' | grep -v 'icc' | grep -v 'gcc' | grep -v 'pgi' | grep -v 'intel' | grep -vi '.bak' | grep -v 'html' | grep -vi 'invsqrta' | grep -v '_invsqrt' | grep -v 'invsqrtdata' | grep -v 'vecinvsqrt' | grep -v 'invsqrtm' | grep -v 'Software' | grep -v 'fast' | grep -v 'invsqrtfracttab' | grep -v 'invsqrtexptab' | grep -v 'version' I finally arrived to 57 entries to invsqrt. Just before start, and since I'm not good at C (F90 addicted), are those 57 entries in only 12 files all that I should have to modify (I expected little more)? Just in case, I'm attaching the output from that load of piped greps. I'll be working on it tonight, and hope tomorrow I'll have more news on it. I'll, if those are the only lines of code to change. Despite of that, I've made a trial without the --disable-x86-64-sse flag for config. The compilation fails at another point now: * /bin/sh ../../../../libtool --mode=compile /usr/bin/gcc -O3 -ffast-math -funroll-all-loops -fpeel-loops -c -o nb_kernel010_x86_64_sse.lo nb_kernel010_x86_64_sse.s libtool: compile: unable to infer tagged configuration libtool: compile: specify a tag with `--tag' make[5]: ** [nb_kernel010_x86_64_sse.lo] Erro 1 * I found some information on this kind of error from libtool on google (something about compiler changing in different parts of compilation process), but I'm not finding a way around this. Does anybody has any idea on this, please? Thanks a lot for everything in advance. Jones include/vec.h:54: real invsqrt(real x) include/vec.h:146:static inline real invsqrt(real x) include/vec.h:466: cos=ip*invsqrt(ipa*ipb);/* 7 */ include/vec.h:674: linv=invsqrt(norm2(src)); src/mdlib/csettle.c:256:axlng = invsqrt(xaksxd * xaksxd + yaksxd * yaksxd + zaksxd * zaksxd); src/mdlib/csettle.c:257:aylng = invsqrt(xaksyd * xaksyd + yaksyd * yaksyd + zaksyd * zaksyd); src/mdlib/csettle.c:258:azlng = invsqrt(xakszd * xakszd + yakszd * yakszd + zakszd * zakszd); src/mdlib/csettle.c:296: cosphi = tmp*invsqrt(tmp); src/mdlib/csettle.c:305: cospsi = tmp2*invsqrt(tmp2); src/mdlib/csettle.c:323: sinthe = (alpa * gama - beta * tmp2*invsqrt(tmp2)) / al2be2; src/mdlib/csettle.c:328: costhe = tmp2*invsqrt(tmp2); src/mdlib/vsite.c:307: c=b*invsqrt(iprod(temp,temp)); src/mdlib/vsite.c:328: invdij = invsqrt(iprod(xij,xij)); src/mdlib/vsite.c:334: b1 = b*invsqrt(iprod(xp,xp)); src/mdlib/vsite.c:380: d=c*invsqrt(iprod(temp,temp)); src/mdlib/vsite.c:631: invl=invsqrt(iprod(xix,xix)); src/mdlib/vsite.c:703: invdij = invsqrt(iprod(xij,xij)); src/mdlib/vsite.c:710: invdp = invsqrt(iprod(xperp,xperp)); src/mdlib/vsite.c:860: invl=invsqrt(iprod(xix,xix)); src/mdlib/clincs.c:199: rlen = invsqrt(tmp0*tmp0+tmp1*tmp1+tmp2*tmp2); src/mdlib/clincs.c:287: mvb = blc[b]*(len - u0*invsqrt(u0)); src/mdlib/clincs.c:364:li-blc[i] = invsqrt(invmass[a1] + invmass[a2]); src/mdlib/clincs.c:586:len = r2*invsqrt(r2); src/tools/gmx_nmeig.c:90: mass_fac=invsqrt(top-atoms.atom[i].m*top-atoms.atom[k].m); src/tools/gmx_nmeig.c:112:mass_fac = invsqrt(top-atoms.atom[j].m); src/tools/gmx_nmeig.c:156: mass_fac=invsqrt(top-atoms.atom[iatom].m*top-atoms.atom[katom].m); src/tools/gmx_nmeig.c:174:mass_fac = invsqrt(top-atoms.atom[j].m); src/tools/calcpot.c:123: rinv1O= invsqrt(rsqO); src/gmxlib/orires.c:302:invr = invsqrt(r2); src/gmxlib/orires.c:460: invr = invsqrt(r2); src/gmxlib/disre.c:160: rt_1 = invsqrt(rt2); src/gmxlib/disre.c:328: weight_rt_1 = invsqrt(rt2); src/gmxlib/ewald_util.c:200: rinv = invsqrt(dr2); src/gmxlib/ewald_util.c:287: rinv = invsqrt(dr2); src/gmxlib/nonbonded/nb_free_energy.c:159:rinv = invsqrt(rsq); src/gmxlib/shift_util.c:237: R_1 = invsqrt(r2); src/gmxlib/shift_util.c:239: R = invsqrt(R_2);
Re: [gmx-users] intel compiler + amd64: help needed.
Hi all. :)
Last message today. It seems that I succeded in switching all invsqrt
functins to a new gmx_invsqrt. Just 57 in the 12 files below:
***
include/vec.h
src/mdlib/csettle.c
src/mdlib/vsite.c
src/mdlib/clincs.c
src/tools/gmx_nmeig.c
src/tools/calcpot.c
src/gmxlib/orires.c
src/gmxlib/disre.c
src/gmxlib/ewald_util.c
src/gmxlib/nonbonded/nb_free_energy.c
src/gmxlib/shift_util.c
src/gmxlib/bondfree.c
*
With this, and with the configure flag --disable-x86-64-sse, The
compilation yelded only warnings. I reproduce they below. Should I be
worried about any of them? The ones involving FFTs, and the ones about
variables being used before declaration do not look too nice to me:
ghat.c(233): warning #266: function declared implicitly
ghat.c(233): warning #967: conversion from int to real={float} ***; sizes do not match
fftgrid.c(227): warning #188: enumerated type mixed with another type
gmx_fft_fftw3.c(96): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(100): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(186): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(190): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(278): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(282): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(370): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(374): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(463): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(467): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(556): warning #1338: arithmetic on pointer to void or function type
gmx_fft_fftw3.c(560): warning #1338: arithmetic on pointer to void or function type
gmx_dielectric.c(150): warning #266: function declared implicitly
gmx_nmtraj.c(134): warning #592: variable bDMA is used before its value is set
Unfortunatelly, as said in the last message, the code still complains
when I try to compile it without the --disable-x86-64-sse flag in the
configure script. Reallt strange is that I don't see why it complains
in one case and not in the other, but the configure fails when tries
to use libtool:
*
/bin/sh ../../../../libtool --mode=compile /usr/bin/gcc -O3
-ffast-math -funroll-all-loops -fpeel-loops -c -o
nb_kernel010_x86_64_sse.lo nb_kernel010_x86_64_sse.s
libtool: compile: unable to infer tagged configuration
libtool: compile: specify a tag with `--tag'
make[5]: ** [nb_kernel010_x86_64_sse.lo] Erro 1
*
Googling this error, I found it related to the changes in the compiler,
but I could not get a way to fix it for gromacs. Did anyone crossed
with this error before, in other context maybe? Any idea on how to fix
it?
Anyway, thanks a lot to everybody for all in advance. If it was not
your help, it would not be possible to get this far already! :) Almost
there now, it seems! :)
Thank you all in advance again.
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] Re: freeenergy calculation
Date: Thu, 01 Jun 2006 15:34:14 +0530 From: lalitha selvam [EMAIL PROTECTED] Subject: [gmx-users] freeenergy calculation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; format=flowed i have completed my simulation.i want to analyse my protein.can u help me how to calculate the free binding energy calculation,which program i should use.i've read gromacs manual 3.3 but i'm in need of any other new analysis are included in version 3.3 or not.so where can i getthe information on availability of more analysis in GROMACS 3.3 version comapred to older version. thanks sir.i'm in hurry.Plz anyone help me. hello, you can use g_sham program (new one in 3.3)to calculate free energy distribution and draw the picture. first, you should prepare a xvg file with three columns. the first is frame time, the second and third are the parameters you want to calculate, for example like this: Time RMSD dist 0 1.2 0.8 1 1.3 1.1 2 0.5 0.9 . . . . . . and then, use the following command: g_sham -f *.xvg -ls you can get the pic, and with -ngrid you can get the high resolution pics. ___ 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] enabling threads in GROMACS
wait for gromacs 4.0. Yang Ye Jayant James Jayasundar wrote: hi all IS it possible to enable threads in gromacs during configuration? Thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790 http://adworks.rediff.com/cgi-bin/AdWorks/sigclick.cgi/www.rediff.com/signature-home.htm/[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
