Re: [gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list)
hi Christian thx for your reply, I've tried that before with the "--enable-thread" option of fftw, with no success, after I turned it off , the installation seemed OK to me. Yours Xin On Nov 9, 2007 1:21 AM, Christian Burisch <[EMAIL PROTECTED]> wrote: > Hi, > > did you try the solutions given to > http://www.gromacs.org/pipermail/gmx-users/2006-August/023545.html ? > > Regards > > Christian > > > > liu xin schrieb: > > Dear GMXers > > I got the error message " cannot compute sizeof (int)" when I tried to > > configure GMX3.3.1 on IBM PPC p575 AIX5.3, this is how I did it: > > > > for fftw2.1.5 > > export CC="xlc_r -q64 -qhot" > > export CXX="xlC_r -q64 -qhot" > > export OBJECT_MODE=64 > > export FFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" > > export CFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" > > ./configure --prefix=/home/usr/programs/fftw215 --enable-float > --enable-mpi > > --enable-thread > > make > > make install > > > > for GMX3.3.1 > > > > export CPPFLAGS=-I/home/usr/programs/fftw215/include > > export LDFLAGS=-I/home/usr/programs/fftw215/lib > > ./configure --prefix=/home/usr/programs/gromacs331mpi --with-fft=fftw2 > > --without-x --disable-fortran --enable-mpi --enable-float > > then I got the following error: > > checking size of int... configure: error: cannot compute sizeof (int), > 77 > > > > have you guys ever experienced this problem before? Any suggestions are > > appreciated! > > > > Yours > > Xin > > > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > Dr. Christian Burisch > Protein Mechanics and Evolution Group > CAS-MPG Partner Institute for Computational Biology > Shanghai Institutes for Biological Sciences > 320 Yue Yang Road > CN-200031 Shanghai > Tel: +86 21 54920478 > Fax: +86 21 54920451 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parallel run on IBM p575 "poe mpi"
Hi guys, just a short question, this is how I run a 8np mpi-mdrun job on my machine: poe /home/usr/programs/gromacs331mpi/bin/mdrun -v -s 8np.tpr --procs 8 -nodes 8 -task_per_node 1 -single_thread yes -eager_limit 65535 -shared_memory but it is much slower than the 1np mode, I havent used poe-mpi before, is there something wrong with my options? Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] "cannot compute sizeof (int), 77" on AIX 5.3 PPC p575 (searched the list)
Dear GMXers I got the error message " cannot compute sizeof (int)" when I tried to configure GMX3.3.1 on IBM PPC p575 AIX5.3, this is how I did it: for fftw2.1.5 export CC="xlc_r -q64 -qhot" export CXX="xlC_r -q64 -qhot" export OBJECT_MODE=64 export FFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" export CFLAGS="-O3 -qarch=pwr4 -qtune=pwr4 -qmaxmem=-1" ./configure --prefix=/home/usr/programs/fftw215 --enable-float --enable-mpi --enable-thread make make install for GMX3.3.1 export CPPFLAGS=-I/home/usr/programs/fftw215/include export LDFLAGS=-I/home/usr/programs/fftw215/lib ./configure --prefix=/home/usr/programs/gromacs331mpi --with-fft=fftw2 --without-x --disable-fortran --enable-mpi --enable-float then I got the following error: checking size of int... configure: error: cannot compute sizeof (int), 77 have you guys ever experienced this problem before? Any suggestions are appreciated! Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining "Cannot compile and link MPI code with mpcc". On 10/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > > Hi, thanks for the time > > I asked my administrator, he told me that there was no mpicc installed > on > > p575, the fore mentioned mpcc was the MPI c compiler, but he is not very > > familiar with the AIX OS either, and I will try to explain my problem > more > > clearly: > > > > a. configure --enable-mpi --prefix=/hpc/gmxmpi > > I got a error message: "checking whether the MPI cc command works... > > configure: error: Cannot compile and link MPI code with mpc" > > > > b. export MPICC=/usr/bin/mpcc > > configure --enable-mpi --prefix=/hpc/gmxmpi > > I got the same error message as (1) > > You need an MPI C compiler. Find out its name. I'd expect b) to work if > you use the right name. Otherwise try ./configure --enable-mpi > MPICC=name_of_mpi_c_compiler > > > c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc > > "--enable-mpi=/usr/bin/mpcc" isn't recognized. Read ./configure --help > > Mark > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi, thanks for the time I asked my administrator, he told me that there was no mpicc installed on p575, the fore mentioned mpcc was the MPI c compiler, but he is not very familiar with the AIX OS either, and I will try to explain my problem more clearly: a. configure --enable-mpi --prefix=/hpc/gmxmpi I got a error message: "checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpc" b. export MPICC=/usr/bin/mpcc configure --enable-mpi --prefix=/hpc/gmxmpi I got the same error message as (1) c. configure --enable-mpi=/usr/bin/mpcc --prefix=/hpc/gmxmpc the configuration ended without error message, but at the end of the configure output, there was no message telling me that I was compiling with MPI support which usaslly does when I compile it on our Linux Cluster. make mdrun I get the error message: "gcc: unrecognized option '-bmaxdata:0x8000" make install-mdrun grompp -f -c -p -o 6np.tpr -sort -shuffle mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory then I got the no MPI support error "GROMACS compiled without MPI support - can't do parallel runs" (4) I checked the Makefile and compared it with the one I successfully compiled on our Linux Cluster, found there was no MPI compiler invoked, for example, the 89th line "AS = gcc", 95th line "CC = gcc", 96th line "CCAS = gcc" etc. in fact, this is the first time we try the AIX OS out, we dont even know which is the MPI compiler, maybe the mpcc is not the MPI compiler... I know many of you guys experienced with installation on AIX, any suggestions ? I am totally a newbie... On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > MPICC is the environment variable (upper case important). It should be set > to the name of your mpi-enabled C compiler. > Cheers, > > ERik > > On Oct 18, 2007, at 4:40 AM, liu xin wrote: > > Hi Erick > you mean export MPICC=mpcc? ok, I will try that > > > > On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > > > Hi, > > > > On Oct 17, 2007, at 7:13 PM, liu xin wrote: > > > > > Thanks for your quick comment David > > > but if I tried > > > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > > it will complain about cant find MPI compiler, but I've already > > > export mpcc=mpicc > > > > > > > Try setting MPICC instead :-) > > > > Cheers, > > > > Erik > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Hi Erick you mean export MPICC=mpcc? ok, I will try that On 10/18/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: > > Hi, > > On Oct 17, 2007, at 7:13 PM, liu xin wrote: > > > Thanks for your quick comment David > > but if I tried > > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > it will complain about cant find MPI compiler, but I've already > > export mpcc=mpicc > > > > Try setting MPICC instead :-) > > Cheers, > > Erik > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install problem on IBM powerpc AIX 5.3
Thanks for your quick comment David but if I tried ./configure --enable-mpi --prefix=/hpc/gromacsmpi it will complain about cant find MPI compiler, but I've already export mpcc=mpicc On 10/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > liu xin wrote: > > Hello everyone > > > > I tried to install gromacs-3.3.1 on our IBM PowerPC with AIX 5.3 OS, > > this is how I've done it: > > ./configure --enable-mpi=/usr/bin --prefix=/hpc/gromacsmpi > Is this the command line you used? Try: > ./configure --enable-mpi --prefix=/hpc/gromacsmpi > > > make mdrun > > make install-mdrun > > > > then I tried to mdrun my system with 6 cpu > > grompp -f md.mdp -c -p -o 6np.tpr -np 6 -shuffle -sort > > mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory > > > > then I get the error message telling me that "the GROMACS was compiled > > with no MPI support", but I can run mdrun with 1 cpu! > > we have installed "Parallel Environment V4.2" and "Parallel Engineering > > and Scienticfic Subroutine Library V3.2" on this machine. I am not > > familiar with the AIX OS, the MPI compiler on our machine is mpcc (I > > dont know for sure) installed in /usr/bin. > > Any suggestions will be REALLY appreciated ! > > > > Yours > > Xin Liu > > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D. > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] install problem on IBM powerpc AIX 5.3
Hello everyone I tried to install gromacs-3.3.1 on our IBM PowerPC with AIX 5.3 OS, this is how I've done it: ./configure --enable-mpi=/usr/bin --prefix=/hpc/gromacsmpi make mdrun make install-mdrun then I tried to mdrun my system with 6 cpu grompp -f md.mdp -c -p -o 6np.tpr -np 6 -shuffle -sort mdrun -v -s 6np.tpr -np 6 -proces 6 -shared_memory then I get the error message telling me that "the GROMACS was compiled with no MPI support", but I can run mdrun with 1 cpu! we have installed "Parallel Environment V4.2" and "Parallel Engineering and Scienticfic Subroutine Library V3.2" on this machine. I am not familiar with the AIX OS, the MPI compiler on our machine is mpcc (I dont know for sure) installed in /usr/bin. Any suggestions will be REALLY appreciated ! Yours Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu "works" in my linux cluster
Thanks for your quick comment Alan :) On 10/9/07, Alan Dodd <[EMAIL PROTECTED]> wrote: > > Yeah. > Check the machinefile tells mpich what you think it does. It looks pretty > certain to be an issue with mpich rather than gromacs. Unfortunately, I > don't use mpich any more because I find LAM better. Standard procedure, > turn up the verbosity on everything, check the outputs, re-read the relevant > manuals. > > ----- Original Message > From: liu xin <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Tuesday, October 9, 2007 1:38:50 PM > Subject: Re: [gmx-users] only one cpu "works" in my linux cluster > > Thanks Alan > in fact I've already added the option -machinefile, here's the script: > > cat $PBS_NODEFILE >/home/liuxin/mpd.hosts > /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts > /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 > /home/liuxin/ > programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 > > I am a little busy today, sorry for replying so late... > > On 10/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote: > > > > Check the MPICH manuals for how to specify the nodes to run on. From > > memory, the option -machinefile lets you do this. > > > > - Original Message > > From: liu xin < [EMAIL PROTECTED]> > > To: Discussion list for GROMACS users > > Sent: Monday, October 8, 2007 1:51:12 PM > > Subject: [gmx-users] only one cpu "works" in my linux cluster > > > > Dear GMXers > > > > this is how I've done it so far: > > grompp -f -c -p -o 12np.tpr -np 12 > > qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s > > 12np.tpr -np 12 ) > > then it seems my mdrun works fine, but when I ssh to each node to check > > the cpu efficiency with "top", I find that there's only one cpu works with > > 12 processes! The other nodes are completely idle. > > > > the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: > > Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 > > x86_64 x86_64 GNU/Linux > > our administrator have installed mpich1.2.7 in the default DIR > > (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, > > so I installed mpich2 in my personal dir. > > I've searched the list, but cant get any solution. Does it have > > something to do with the kernel or there's some conflict between mpich1 and > > 2, or something else? > > > > This is the first time I build up a Linux Cluster on my own, ANY > > suggestions are appreciated ! > > > > Xin Liu > > > > > > -- > > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user > > panel<http://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+>and > > lay it on us. > > > > ___ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > Pinpoint customers > <http://us.rd.yahoo.com/evt=48250/*http://searchmarketing.yahoo.com/arp/sponsoredsearch_v9.php?o=US2226&cmp=Yahoo&ctv=AprNI&s=Y&s2=EM&b=50>who > are looking for what you sell. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] only one cpu "works" in my linux cluster
Thanks Alan in fact I've already added the option -machinefile, here's the script: cat $PBS_NODEFILE >/home/liuxin/mpd.hosts /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 /home/liuxin/ programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 I am a little busy today, sorry for replying so late... On 10/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote: > > Check the MPICH manuals for how to specify the nodes to run on. From > memory, the option -machinefile lets you do this. > > ----- Original Message > From: liu xin < [EMAIL PROTECTED]> > To: Discussion list for GROMACS users > Sent: Monday, October 8, 2007 1:51:12 PM > Subject: [gmx-users] only one cpu "works" in my linux cluster > > Dear GMXers > > this is how I've done it so far: > grompp -f -c -p -o 12np.tpr -np 12 > qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s > 12np.tpr -np 12 ) > then it seems my mdrun works fine, but when I ssh to each node to check > the cpu efficiency with "top", I find that there's only one cpu works with > 12 processes! The other nodes are completely idle. > > the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: > Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 > x86_64 GNU/Linux > our administrator have installed mpich1.2.7 in the default DIR > (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so > I installed mpich2 in my personal dir. > I've searched the list, but cant get any solution. Does it have something > to do with the kernel or there's some conflict between mpich1 and 2, or > something else? > > This is the first time I build up a Linux Cluster on my own, ANY > suggestions are appreciated ! > > Xin Liu > > > -- > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user > panel<http://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+>and > lay it on us. > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] only one cpu "works" in my linux cluster
Dear GMXers this is how I've done it so far: grompp -f -c -p -o 12np.tpr -np 12 qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr-np 12 ) then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle. the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir. I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else? This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated ! Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)
yes, I run my work in a queueing system: qsub -l nodes=*,walltime ***:**:** mdrun.sh and I will get two file, one for the standard output one for the standard error output, as soon as my script get running but for my case, there nothing in the error file, and everything in the output file seemed ok. On 10/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > liu xin wrote: > > Thanks Mark > > > > But there's no standard error output at all for my problem, > > Are you running a batch job in a queueing system and explicitly or > implicitly asking that standard error not be returned? > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)
Thanks Florian this is how I tried to invoke the mdrun with mpirun: mpirun -nolocal -machinefile $PBS_NODESFILE mdrun -np * -v -s ... the administrator said the three options for mpirun must be added (-nolocal, -machinefile, $PBS_NODESFILE) now I'm trying to follow the steps in the webpage you gave to me On 10/1/07, Florian Haberl <[EMAIL PROTECTED]> wrote: > > Hi, > > On Sunday, 30. September 2007 19:12, liu xin wrote: > > Thanks Mark > > > > But there's no standard error output at all for my problem, it seems > mdrun > > stagnated at this point, I dont know if anybody had met this situation > > before...and now I'm compiling LAMMPI as you suggested, hope this works > for > > me. > > does your calculation run with PBS or any queuing system? > You can try to run mpirun or others like mpiexec with a verbose option. > > In your previous mail you wrote something about running jobs with mpd, is > it > your queuing system > (http://www-unix.mcs.anl.gov/mpi/mpich1/docs/mpichntman/node39.htm), i > don`t > know if its outdated (webpage seems so). > > > Here gromacs run without problems with different mpi implementations also > with > intel-mpi, mvapich. > > > > > On 10/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > > liu xin wrote: > > > > Dear GMXers > > > > > > > > my mdrun stops when I try to do it with 8 nodes, but there's no > error > > > > message, here's the end of the md0.log: > > > > > > The log file won't be helpful if the problem is outside of GROMACS, > and > > > the fact that it isn't helpful is strongly diagnostic of that. You > need > > > the standard error to diagnose what your system problem is. > > > > > > > "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. > Fraaije > > > > LINCS: A Linear Constraint Solver for molecular simulations > > > > J. Comp. Chem. 18 (1997) pp. 1463-1472 > > > > --- Thank You --- > > > > > > > > > > > > Initializing LINear Constraint Solver > > > > number of constraints is 3632 > > > > average number of constraints coupled to one constraint is 2.9" > > > > > > > > > > > > I also tried 6 nodes or 10 nodes, but mdrun always stops here, > there's > > > > no problem if I ran it by -np 4. > > > > I searched the list, I found some people said that this probably > > > > because the MPI version, currently, we used the 1.2.7 > > > > > > MPICH for GROMACS is not supported at all. Try LAM if you suspect the > > > MPI install, and I would suspect it. > > > > > > Mark > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > Greetings, > > Florian > > -- > > --- > Florian Haberl > Computer-Chemie-Centrum > Universitaet Erlangen/ Nuernberg > Naegelsbachstr 25 > D-91052 Erlangen > Telephone: +49(0) − 9131 − 85 26581 > Mailto: florian.haberl AT chemie.uni-erlangen.de > > --- > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MPIRUN problem when switched to 8 np (searched the list)
Thanks Mark But there's no standard error output at all for my problem, it seems mdrun stagnated at this point, I dont know if anybody had met this situation before...and now I'm compiling LAMMPI as you suggested, hope this works for me. On 10/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > liu xin wrote: > > Dear GMXers > > > > my mdrun stops when I try to do it with 8 nodes, but there's no error > > message, here's the end of the md0.log: > > The log file won't be helpful if the problem is outside of GROMACS, and > the fact that it isn't helpful is strongly diagnostic of that. You need > the standard error to diagnose what your system problem is. > > > "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije > > LINCS: A Linear Constraint Solver for molecular simulations > > J. Comp. Chem. 18 (1997) pp. 1463-1472 > > --- Thank You --- > > > > > > Initializing LINear Constraint Solver > > number of constraints is 3632 > > average number of constraints coupled to one constraint is 2.9" > > > > > > I also tried 6 nodes or 10 nodes, but mdrun always stops here, there's > > no problem if I ran it by -np 4. > > I searched the list, I found some people said that this probably because > > the MPI version, currently, we used the 1.2.7 > > MPICH for GROMACS is not supported at all. Try LAM if you suspect the > MPI install, and I would suspect it. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MPIRUN problem when switched to 8 np (searched the list)
Dear GMXers my mdrun stops when I try to do it with 8 nodes, but there's no error message, here's the end of the md0.log: "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije LINCS: A Linear Constraint Solver for molecular simulations J. Comp. Chem. 18 (1997) pp. 1463-1472 --- Thank You --- Initializing LINear Constraint Solver number of constraints is 3632 average number of constraints coupled to one constraint is 2.9" I also tried 6 nodes or 10 nodes, but mdrun always stops here, there's no problem if I ran it by -np 4. I searched the list, I found some people said that this probably because the MPI version, currently, we used the 1.2.7 It is weird that another cluster, install mpich1.2.7, goes well with mdrun. I also installed mpich2 in my personal directory (I have no administrator privilege on the cluster...), but it keeps on complaining the "mpd" setting, though I created a .mpd.conf file as it told me in my home directory. Should I install mpich2 by root? Is there any conflict if I installed both mpich1 and mpich2? I've searched the list but cant find something useful to solve my problem Any suggestions will be REALLY appreciated! Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to Install GMX V3.3.1 with Intel fortran compiler?
Dear GMX-users: I've searched the list but couldnt find something usful for me, and this is how I did it so far : source /opt/intel/fce/version/bin/ifortvars.sh export F77=ifort export CPPFLAGS=-I/home/xin/programs/fftw312/include export LDFLAGS=-L/home/dong/programs/fftw312/lib configure --prefix=/home/xin/programs/gromacs331 --enable-fortran --enable-mpi make mdrun make install-mdrun after the installation, I tried to do the mdrun: mpirun -np 2 /home/xin/programs/gromacs331/mdrun -s ... and then I got the following error message: error while loading shared libraries: libsvml.so: cannot open shared object file: No such file or directory The OS of my pc is SUSE 9.3. And I found that the "missing" file, libsvml.so, was in /opt/intel/fce/version/lib Is there something wrong with my steps? or shoould I add some FFLAGS? I am not very familiar with fortran and Linux, any suggestions will be appreciated! Xin Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Why did it start from the very beginning???
Hi Mark I checked my mdp file, the flags for nstvout and nstfout are all zero, this must be the problem. Thank you for your suggestions! Yours Xin On 4/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: liu xin wrote: > Hi GMX users > > My 2ns simulation crashed accidentally, gmxcheck said my previous > simulation was stopped at 1400 ps, then I used the tpbconv to generate a > new tpr to restart it from the previous ending point: > "tpbconv -f -e -s -o new.tpr" > but I found the output message of tpbconv said: > "100 steps (2000 ps) remaining from first run. > Writing statusfile with starting step 0 and length100 > steps... > time 0.000 and length 2000.000ps" > and if I use the new.tpr, the simulation will run another 2ns! I doubt > that this new.tpr will restart my simulation from the beginning. Then I > tried -time 1300, -time 1000, -until 2000, the output message was the same. > Did I use the tpbconv in a wrong way? You need a trajectory frame with both positions and velocities... (and an energy frame from its file if you want an exact continuation of pressure-coupling or N-H T-coupling) I guess that only your first frame satisfies this. Consult the n???out flags in your original mdp file for the frequency with which you are writing velocities. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Why did it start from the very beginning???
Hi GMX users My 2ns simulation crashed accidentally, gmxcheck said my previous simulation was stopped at 1400 ps, then I used the tpbconv to generate a new tpr to restart it from the previous ending point: "tpbconv -f -e -s -o new.tpr" but I found the output message of tpbconv said: "100 steps (2000 ps) remaining from first run. Writing statusfile with starting step 0 and length100 steps... time 0.000 and length 2000.000 ps" and if I use the new.tpr, the simulation will run another 2ns! I doubt that this new.tpr will restart my simulation from the beginning. Then I tried -time 1300, -time 1000, -until 2000, the output message was the same. Did I use the tpbconv in a wrong way? Thanks in advance! Yours Xin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Your computational box has shrunk too much!
Hello GMX-usersWhen I wanted to analysis the hbond interaction between the protein and the dppc headgroup, I got the following error:Program g_hbond, VERSION 3.3.1Source code file: gmx_hbond.c, line: 631 Fatal error:Your computational box has shrunk too much.g_hbond can not handle this situation, sorry.I found that if I set -e and -b option, for example, first I use g_hbond -e 2050, then use g_hbond -b 2050, I can get through the problem.Was there something I did wrong here? ___ 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] HBond frequency
Thanks everyone :)Finally I've got the map using xpm2psI'm new to gromacs and Linux, so it will take some time to learn the script language. On 10/1/06, Erik Marklund <[EMAIL PROTECTED]> wrote: - Original Message -From: "David van der Spoel" <[EMAIL PROTECTED]>To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>Sent: Saturday, September 30, 2006 2:37 AMSubject: Re: [gmx-users] HBond frequency> liu xin wrote:>> Thanks, but when ever I used ACDsee to visualize the generated hbmap.xpm,>> I've got nothing, and ACDsee keeps on telling me that "Bad or>> unrecognized image header".>>> Try the gimp or use xpm2ps first.>> --> David. Or analyze the data by other means. The image data is uncompressed andstored row-wise in the file, making it relatively easy to extract, in yourcase, hbond frequencies, using most any scripting language. /Erik> > 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 list gmx-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-usersPlease don't post (un)subscribe requests to the list. Use thewww 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] HBond frequency
Thanks, but when ever I used ACDsee to visualize the generated hbmap.xpm, I've got nothing, and ACDsee keeps on telling me that "Bad or unrecognized image header".On 9/30/06, Erik Marklund <[EMAIL PROTECTED]> wrote: - Original Message -From: "Mark Abraham" <[EMAIL PROTECTED]>To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>Sent: Friday, September 29, 2006 1:28 AMSubject: Re: [gmx-users] HBond frequency> liu xin wrote:>> Hello GMX users:>>>> Just a quick question: how can I get the frequency of each HBond? >>>> From hbond.ndx we can get a list of hbonds, e.g. hbonds between protein>> and drug, if I want to check the frequency of each hbond between the two>> components respectively, how can I realize it? >> man g_hbond and look for -xbmAlmost. -hbm is the flag you would want to use./Erik>> Mark> ___> gmx-users mailing list gmx-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-usersPlease don't post (un)subscribe requests to the list. Use thewww 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] HBond frequency
Hello GMX users:Just a quick question: how can I get the frequency of each HBond?From hbond.ndx we can get a list of hbonds, e.g. hbonds between protein and drug, if I want to check the frequency of each hbond between the two components respectively, how can I realize it? ___ 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] Re: Simulation problem with extended membrane system!
Thanks Chris, I really appreciate your help!I've got my extended membrane system regarding your note, and now I'm testing it with my GPCR. I am still not very familiar with the script, I think it will take some time to learn. Thanks again!On 9/13/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:>If I solvate my GPCR into the DPPC128 system using genbox, there are only >about 50 lipids left, which I think are too few, so I want a larger starting>structure.>According to your note, when I did step 3, loaded my DPPC183 system to VMD,>I found the edges lined up poorly, there is are gaps between two periodic >cells. I also try other system like DPPC200, DPPC150, but only the original>dppc128 system, I've equilibrated it for 2ns, have no gap between two>periodic cells.>So, I will try another starting structure, like POPC, DMPC or your POPE. But >I still can't figure out why there are gaps when using genbox to extend the>DPPC system.It's because any overlap causes an entire lipid to be removed.If you don't want to equilibrate, try exactly doubling your system size in x and y. That should work perfectly.___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww 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] Re: Simulation problem with extended membrane system!
If I solvate my GPCR into the DPPC128 system using genbox, there are only about 50 lipids left, which I think are too few, so I want a larger starting structure.According to your note, when I did step 3, loaded my DPPC183 system to VMD, I found the edges lined up poorly, there is are gaps between two periodic cells. I also try other system like DPPC200, DPPC150, but only the original dppc128 system, I've equilibrated it for 2ns, have no gap between two periodic cells. So, I will try another starting structure, like POPC, DMPC or your POPE. But I still can't figure out why there are gaps when using genbox to extend the DPPC system.On 9/9/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >According to your suggestion, I did a energy minimization and then a MDS>with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were>simulated with no constraint. This time I use semiisotropic pressure >coupling with tau_p=5. The system will be equilibrated with water>constrained for 1ns, do you think it's enough?It will be more than enough. Use vmd to watch the trajectory. It's importantactually look at the structures. >The reason why I want to extend the system is because that I've got a GPCR,>and I want to simulate it in a DPPC membrane environment, but the z>dimension of the membrane, downloaded from Dr. Tielman's websit, was not >large enough, when I align the protein to the z axis of the membrane I find>the two ends of the protein are poking out of both water layers.In this case you may not need to extend the lipid. Why not just use editconf to increase the z dimension while keeping the x and y constant. Then insert yourprotein, re-solvate, re-equilibrate, and your into production. If your lipidtakes up a maximum amout of space D in the xy-plane, then x and y need only be equal to [D + 2*max(LJ cutoff, Coulombic real-space cutoff) + some extra amountin case the protein fluctuations make it larger during the simulation].>Back to the previous question, after solvate the lipids in water, can I >remove the water placed in the membrane with excel instead of script? Cause>with editconf we can know the z dimension of the lipids_only system, let's>say 6, so if I center the whole system with 0 0 0, the water molecules with >z coordinates below 3 and above -3 will be excluded. If I'm right, I think>excel can do it too, or the scripts have some advantages?Sure you can use excel, but I am not sure how that is going to affect your formatting or how gromacs responds to formatting (i.e. spaces / tabs / thenumber of each) So scrips have 2 advantages: 1)formatting is easily maintained,2)if you need to do it a second time you just type one command. After using excel (or a script) make sure to update you topology file to indicate the numberof waters.___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] Re: Simulation problem with extended membrane system!
Hi ChrisThank you for your note!According to your suggestion, I did a energy minimization and then a MDS with "freezegrps=SOL, freezedim=N, N, Y", the rest of the system were simulated with no constraint. This time I use semiisotropic pressure coupling with tau_p=5. The system will be equilibrated with water constrained for 1ns, do you think it's enough? The reason why I want to extend the system is because that I've got a GPCR, and I want to simulate it in a DPPC membrane environment, but the z dimension of the membrane, downloaded from Dr. Tielman's websit, was not large enough, when I align the protein to the z axis of the membrane I find the two ends of the protein are poking out of both water layers. Back to the previous question, after solvate the lipids in water, can I remove the water placed in the membrane with excel instead of script? Cause with editconf we can know the z dimension of the lipids_only system, let's say 6, so if I center the whole system with 0 0 0, the water molecules with z coordinates below 3 and above -3 will be excluded. If I'm right, I think excel can do it too, or the scripts have some advantages? Thank you againOn 9/8/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: Having actually looked back at my notes, here is what I did to extend pope.pdbinto a larger system. However, the suggestion that I posted last time should work just as well.1. Remove all waters2. Duplicate the box until your heart's content. Make it larger than youactually want because the box will collapse to some extent.3. MD with Z-only posre on lipid head groups (X and Y force components = zero). This step must be done with constant pressure (In this procedure, make sure touse isotropic pressure coupling so that the box max and min z don't come intocontact with the membrane).NOTE for step 3: It is assumed that your edges line up with each other. Load the system into vmd and show periodic unit cells to make sure. If they line uppoorly then I would find a new starting PDB. However, pope.pdb lines up well.4. Adjust the z-dimension to what you want it to be, center your membrane in the z if you want to.5. solvate the system.6. Remove any waters that were placed within the membrane7. energy minimize8. posre run as before to allow the water to adjust to the membrane surfaces.However, during this run (and all the rest of the steps) I use semiisotropic Pcoupling.9. equilibration phase without any position restraints10. production run.If you are going to add protein, you could do that with the results of step 4since most procedures involve stripping out any waters anyway. Again, the procedure that I outlined previously should work, but I have nottested that procedure, only this one.___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
[gmx-users] Re: Simulation problem with extended membrane system!
Hello Chris So you mean to do a constrained MDS to let the lipids "fill the gaps" between the box edges and lipids, after that do a unconstrained MDS, then we'll get a fine structure, am I right? Thank you very much, I'll try that Xin Liu On 9/7/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: If you can't write a script, then do the minimization and equilibration with water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or use constraints in the z dimension (posre.itp force constant 1000 along z and 0 along x and y). This will stop it from going into the membrane. Before you start, sort the initial PDB according to z (you could do this in excel), remove any waters that you don't want, resort according to original order, and run pdb2gmx. Note that pope.pdb does have a small cluster of waters in the membrane. ___ 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] Simulation problem with extended membrane system!
Hi ChrisThank you for your suggestions!These days I also tried anisotropic and semiisotropic for my simulation, but I still got the same result, so I wonder maybe there's something wrong with my initial structure, but it will take time to check it out. I'm trying to use the method you suggested, I searched the list, find there is some scripts offered by other users, but I'm new to Linux and gromacs, I've got no idea which one to use and how to use it. So would you please send me a sample? Thank you very much for your helpXin LiuOn 9/5/06, [EMAIL PROTECTED] < [EMAIL PROTECTED]> wrote:It is unclear why your second method works for you. However, given that it does, just use genbox -cs spc216.gro -cp 183_system_that_worked.gro -box 9.2 9.2 8.3and then use your own script to remove any spc waters that were put inside themembrane and modify the nubers in your topology file accordingly. I imagine that your first attempt didn't work since an entire dppc molecule isremoved upon a single collision and this will lead to "holes" in your membranethat will quickly fill with water. Of course this should also have happened in your second attempt... I am not sure what was different there.You need semiisotropic pressure coupling and you need to stop every once and awhile and remove any water molecules that are inside the membrane. Note that isotropic Pcoupling in a membrane system (as you have been doing) has thepotential to provide a surface tension (or the opposite) that you have not beenintentionally including and so you can expect your membrane to behave differently. Chris.___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww 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] Simulation problem with extended membrane system!
Dear GMX-users:I met a problem when doing simulation with the membrane , here's what I've done so far:I download the dppc128.pdb file and dppc.top files from Dr. Tielman's website, equilibrated this dppc128 system for 10ns, I checked the final structure with VMD, everything seemed ok. Then I extended this system to a larger one with thicker water layers and more lipid molecules with the following commands: editconf -f dppc128.pdb -o dppc128_center.pdb -center 0 0 4.1genbox -cs dppc128_center.pdb -o larger_box.pdb -box 9.2 9.2 8.3So I got a membrane system with 183 lipid molecules and 12752 SOL molecules, then I did a simulation with this system for 1ns. But when I check the final structure, I find the water molecules, at the edge of the box, spread across the Z axis, but not insert into the lipid molecules. It seems that the water molecules are all around the lipid molecules in a cubic box. At the same time, I find the arrangement of the lipid molecules are disordered, the lipid leaflets get closer, and become crooked, not as straight as before. It looks like that the whole system is compressed across the Z axis. And what's weird to me is that if I don't extend the water, make the two water layers as thick as before, just extend the dppc128 system to a dppc183 system, then doing simulation, there is no such phenomenon. Is it because I've got too much water? Or is there something wrong with my method? Here's my mdout.mdp file:; VARIOUS PREPROCESSING OPTIONStitle = DPPC; Preprocessor - specify a full path if necessary. cpp = /lib/cppinclude = define = ; RUN CONTROL PARAMETERSintegrator = md; Start time and timestep in pstinit = 0 dt = 0.002nsteps = 50; For exact run continuation or redoing part of a runinit_step = 0; mode for center of mass motion removalcomm-mode = Linear ; number of steps for center of mass motion removalnstcomm = 1; group(s) for center of mass motion removalcomm-grps = ; LANGEVIN DYNAMICS OPTIONS; Friction coefficient (amu/ps) and random seed bd-fric = 0ld-seed = 1993; ENERGY MINIMIZATION OPTIONS; Force tolerance and initial step-sizeemtol = 10emstep = 0.01; Max number of iterations in relax_shells niter = 20; Step size (ps^2) for minimization of flexible constraintsfcstep = 0; Frequency of steepest descents steps when doing CGnstcgsteep = 1000 nbfgscorr = 10; OUTPUT CONTROL OPTIONS; Output frequency for coords (x), velocities (v) and forces (f)nstxout = 2500nstvout = 1000nstfout = 0 ; Checkpointing helps you continue after crashesnstcheckpoint = 1000; Output frequency for energies to log file and energy filenstlog = 1000nstenergy = 1000 ; Output frequency and precision for xtc filenstxtcout = 0xtc-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 groupsenergygrps = SOL DPPC; NEIGHBORSEARCHING PARAMETERS; nblist update frequencynstlist = 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 = 1.0domain-decomposition = no; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostaticscoulombtype = PMErcoulomb-switch = 0rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction fieldepsilon_r = 1epsilon_rf = 1; Method for doing Van der Waalsvdw-type = Cut-off; cut-off lengths rvdw-switch = 0rvdw = 1.0; Apply long range dispersion corrections for Energy and PressureDispCorr = No; Extension of the potential lookup tables beyond the cut-off table-extension = 1; Seperate tables between energy group pairsenergygrp_table = ; Spacing for the PME/PPPM FFT gridfourierspacing = 0.12; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0fourier_ny = 0fourier_nz = 0; EWALD/PME/PPPM parameterspme_order = 4ewald_rtol = 1e-05ewald_geometry = 3d epsilon_surface = 0optimize_fft = yes; GENERALIZED BORN ELECTROSTATICS; Algorithm for calculating Born radiigb_algorithm = Still; Frequency of calculating the Born radii inside rlist nstgbradii = 1; Cutoff for Born
[gmx-users] Could anybody post a sample.mdp for protein-membrane-aqueous simulation ?
Dear GROMACS UsersI'm doing a simulation of a protein-membrane-aqueous system, I'm not very familiar with the .mdp files of this kind, so, could anybody kind enough send me two sample.mdp files for position restraint and molecular dynamic? The membrane type I chosen is DPPC. Thanks in advance! ___ 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
