Re: [gmx-users] compile GMX source code by VC 6.0
Hi, Find them in /include Yang Ye 主月 ：） wrote: > Hi: > I tried to compile GMX source code by VC 6.0. > I found the main function of MD simulation is in mdrun.c. And then i > compiled it as main file. > But some varier type my compiler can not find . Such as : > LONG; > TCHAR; > BSTR; > BOOL; > DATE; > How can i fix it ! > thanks a lot > > > ___ > 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] compile GMX source code by VC 6.0
Hi: I tried to compile GMX source code by VC 6.0. I found the main function of MD simulation is in mdrun.c. And then i compiled it as main file. But some varier type my compiler can not find . Such as : LONG; TCHAR; BSTR; BOOL; DATE; How can i fix it ! thanks a lot ___ 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] dialanine
Hi Debashis, Parameters and .pdb file are different things. To generate a structure for dialanine you can use prodrg, pymol, write it by hand or search the web. If you want to use your own force field parameters you have to write a .itp file. Check the gromacs manual for that. TsjerkOn 6/8/06, Debashis Dutta <[EMAIL PROTECTED]> wrote: Hi, I am seeking help in creating the .pdb file for a dialaninemolecule using the databank. I have the parameters for a single alaninemolecule. how do i go from here.ThanksDebashis ___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-users Please 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-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical Chemistry University of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336 ___ 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] Ambconv package
Hello all, I am running my MD simulation with AMBER package as of now. But I want to switch to Gromacs package, which I have installed on my system. In order to convert Amber generated topology file to be understood by Gromacs, I am searching for AMBCONV package. But Somehow I couldnt find it on Internet, I will be highly obliged if you help me in this regard to get that from Internet, (I mean where can I get that?) Thanking You, Amit Jain ___ 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] Freezing part of the molecules!!!
Can you use this freezegroups function during a minimizaiton? (say if you wanted to minimize solvent around your protein, while keeping the protein fixed?) David van der Spoel wrote: Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group and so on. Remember to use the numbering as it is in the gro file. This you can do with "make_ndx -f your_gro_file.gro" 2. Add the folling to your mdp file: freezegrps = Group1 Group2 Group3 Group4 Group5 freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Note that for each group defined as freezegroup you need to specify the dimensions that you want to freeze (x y z). This is done with either Y or N. So if you want only to freeze Group1 in the z-direction you write: freezegrps = Group1 freezedim = N N Y All the best, Soren Just as a warning: please note that combining: constraints + freeze groups + pressure coupling will give undefined results. Quoting Marcelo Fabricio Masman <[EMAIL PROTECTED]>: Hi all!!! I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest. For example, my protein group has 5 protein chains with 42 residues each of them. I would like to freeze (in all directions) the alfa Carbon atoms for residues 18-42 for each chain. Does somebody know if it is possible to do such thing with GROMACS? Can somebody help me? Thanks a lot, in advance Marcelo - This mail sent through IMP: http://horde.org/imp/ ___ 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] dialanine
Hi, I am seeking help in creating the .pdb file for a dialanine molecule using the databank. I have the parameters for a single alanine molecule. how do i go from here. Thanks Debashis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS with MPICH on Sun Cluster
Alok wrote: I tried ldd `which mdrun_mpi` output is :- ### $ldd `which mdrun_mpi` libnsl.so.1 => /lib64/libnsl.so.1 (0x002a95687000) libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x002a9579e000) libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x002a95b2e000) libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x002a95c8e000) libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x002a95d98000) libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x002a95eb2000) libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x002a95fc3000) libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x002a960cc000) libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x002a962c) libz.so.1 => /usr/lib64/libz.so.1 (0x002a964d9000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x002a965e7000) libm.so.6 => /lib64/tls/libm.so.6 (0x002a966fc000) libc.so.6 => /lib64/tls/libc.so.6 (0x002a96884000) libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x002a96ac8000) libdl.so.2 => /lib64/libdl.so.2 (0x002a96be2000) /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 (0x002a95556000) ## what can we conclude from this output ?? there is no FFT, no MPI, so these are hard linked into the program. That means you can not have problems with those at least. I will try "make CFLAGS=-g install" option alsothen i will come back to you. Thanks a lot ! best regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Thursday, June 08, 2006 8:25 PM Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster Alok wrote: I tried mpirun mdrun_mpi -h but I got same error message [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_29243: p4_error: : 0 Thanks for your kind attention. Apart from upgrading to FFTW3 and GROMACS 3.3.1, you could try ldd `which mdrun` to check which libraries are being used. Maybe you are mixing different MPI libraries (i.e. compile with one, run with another). You can also compile by make distclean make CFLAGS=-g install in order to be able to debug -- 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 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] g_com
Hi,Have a look at g_traj, in particular the -com option.Cheers,ErikOn Jun 8, 2006, at 5:31 PM, Alessandro Mattozzi wrote:Hi Is there any way for calculating the trajectory of the center of mass ? Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___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] g_com
Title: g_com Hi Is there any way for calculating the trajectory of the center of mass ? 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
Re: [gmx-users] GROMACS with MPICH on Sun Cluster
I tried ldd `which mdrun_mpi` output is :- ### $ldd `which mdrun_mpi` libnsl.so.1 => /lib64/libnsl.so.1 (0x002a95687000) libXm.so.3 => /usr/X11R6/lib64/libXm.so.3 (0x002a9579e000) libXt.so.6 => /usr/X11R6/lib64/libXt.so.6 (0x002a95b2e000) libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x002a95c8e000) libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x002a95d98000) libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x002a95eb2000) libXp.so.6 => /usr/X11R6/lib64/libXp.so.6 (0x002a95fc3000) libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x002a960cc000) libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x002a962c) libz.so.1 => /usr/lib64/libz.so.1 (0x002a964d9000) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x002a965e7000) libm.so.6 => /lib64/tls/libm.so.6 (0x002a966fc000) libc.so.6 => /lib64/tls/libc.so.6 (0x002a96884000) libXmu.so.6 => /usr/X11R6/lib64/libXmu.so.6 (0x002a96ac8000) libdl.so.2 => /lib64/libdl.so.2 (0x002a96be2000) /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 (0x002a95556000) ## what can we conclude from this output ?? I will try "make CFLAGS=-g install" option alsothen i will come back to you. Thanks a lot ! best regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Thursday, June 08, 2006 8:25 PM Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster Alok wrote: I tried mpirun mdrun_mpi -h but I got same error message [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_29243: p4_error: : 0 Thanks for your kind attention. Apart from upgrading to FFTW3 and GROMACS 3.3.1, you could try ldd `which mdrun` to check which libraries are being used. Maybe you are mixing different MPI libraries (i.e. compile with one, run with another). You can also compile by make distclean make CFLAGS=-g install in order to be able to debug -- 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 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] drift of simulation cell
Qing Zhu wrote: Thanks for the quick reply, but now the situation is we already finished a very long run before we realized this problem. So what I want to know is for the given trajectory we have now, can we correct it in retrospect, or if anything from the simulation might be salvaged. you can do it with trjconv, but if a lot of motion has gone into the center of mass motion of the water and/or membrane that means you have simulated at a lower temperature than what you think you have. Compare the kinetic energy of the membrane (from trr file) and from the center of mass motion. Use g_traj When you said turning off the center of mass motion for membrane and water separately, is it to specify membrane and water separately instead of the whole system in "comm_grps" option? Thanks Qing Zhu David van der Spoel wrote: Qing Zhu wrote: Hi All, I am using gromacs to simulate a lipid/cholesterol mixed membrane. When I looked at the trajectory using VMD, the whole simulation cell laterally drifted very fast, and it looked like center of mass motion. But when I set up the simulation, I did turn off the center of mass motion. I don't know where this drifting motion came from, and it had huge influence on the calculations of system diffusion property. So does anyone know how to remove this kind of fast drifting motion from the trajectory so that I can do some correct calculations on diffusion. you want to turn off center of mass motion for membrane and water separately. If you look closer you will probaböy see they move in opposite directions. Thanks Qing Zhu ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS with MPICH on Sun Cluster
Alok wrote: I tried mpirun mdrun_mpi -h but I got same error message [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_29243: p4_error: : 0 Thanks for your kind attention. Apart from upgrading to FFTW3 and GROMACS 3.3.1, you could try ldd `which mdrun` to check which libraries are being used. Maybe you are mixing different MPI libraries (i.e. compile with one, run with another). You can also compile by make distclean make CFLAGS=-g install in order to be able to debug -- 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] drift of simulation cell
Thanks for the quick reply, but now the situation is we already finished a very long run before we realized this problem. So what I want to know is for the given trajectory we have now, can we correct it in retrospect, or if anything from the simulation might be salvaged. When you said turning off the center of mass motion for membrane and water separately, is it to specify membrane and water separately instead of the whole system in "comm_grps" option? Thanks Qing Zhu David van der Spoel wrote: Qing Zhu wrote: Hi All, I am using gromacs to simulate a lipid/cholesterol mixed membrane. When I looked at the trajectory using VMD, the whole simulation cell laterally drifted very fast, and it looked like center of mass motion. But when I set up the simulation, I did turn off the center of mass motion. I don't know where this drifting motion came from, and it had huge influence on the calculations of system diffusion property. So does anyone know how to remove this kind of fast drifting motion from the trajectory so that I can do some correct calculations on diffusion. you want to turn off center of mass motion for membrane and water separately. If you look closer you will probaböy see they move in opposite directions. Thanks Qing Zhu ___ 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] GROMACS with MPICH on Sun Cluster
I tried mpirun mdrun_mpi -h but I got same error message [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_29243: p4_error: : 0 Thanks for your kind attention. Regards, Alok - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Thursday, June 08, 2006 8:14 PM Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster Alok wrote: Hi, I am trying to run GROMACS in parallel on a SUN Cluster with MPICH. I had installed FFTW 2.1.5 and Gromacs 3.2.1 without any error massage, but when i tried to use mdrun_mpi (or even mdrun_mpi -h) I got the following error message. how about mpirun mdrun -h [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_1870: p4_error: : 0 I followed the follwing procedure for installing FFTW 2.1.5 and GROMACS 3.2.1. First of all I set the PATH for MPICH files in my .profile file. PATH=/opt/mpichdefault-1.2.6/bin:$PATH PATH=/opt/mpichdefault-1.2.6/lib:$PATH PATH=/opt/mpichdefault-1.2.6/include:$PATH ### FFTW 2.1.5 # export MPICC=mpicc export LIBS="-lmpich -lfmpich -lpmpich" export MPILIBS="-L/opt/mpichdefault-1.2.6/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include" export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib" ./configure --enable-float --prefix=/users/bsbe/phd/alokjain/install/fftw --enable-mpi make make install # ## GROMACS 3.2.1 export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib -L/users/bsbe/phd/alokjain/install/fftw/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include -I/users/bsbe/phd/alokjain/install/fftw/include" ./configure --enable-mpi --prefix=/users/bsbe/phd/alokjain/install/gromacs --program-suffix=_mpi make make install # Any ideas regarding what is going wrong? Please let me know if you need more information... Thank you very much in advance, regards, Alok jain ___ 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 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] configuration, make, installation problem
Mark Abraham wrote: I use modules intel-cc/9.0.031 and fftw/2.1.5-intel-9.0 and scsl/1.6.0.0 (the latter means you are using linear algebra stuff optimized for this machine instead of generic BLAS/LAPACK... not hugely important though) and for non-MPI have used The reason I'm using fftw/2.1.5 was to avoid a problem with needing the single-precision version named appropriately. I expect with double precision you may be able to use fftw/3.0.1 out of the box... I will play with this some time and hassle the admins in due course if necessary. 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] configuration, make, installation problem
Nevena Todorova wrote: Hi there, i am trying to install (double precision, mpi )Gromacs 3.3 on an SGI Altix system and during this process i encounter few problems. I observe that you are trying to install 3.3 on the APAC ac machine. If you want a double precision MPI version, I'm sure the admins will do that for you in no time flat - they've always done so for me, as evidenced by the plethora of pre-release 3.3 versions they still have lying around! (see "module avail") Unless you need 3.3, you may as well ask for 3.3.1 too! I configure the system using the commmand: ./configure --enable-mpi --enable-shared --disable-nice --disable-float --prefix=$HOME/g-3.3 --program-suffix=_d_mpi --with-fft=fftw2 and it seems to be running without problems untill the end where it stops without an output line for a successful configuration. It is not giving me an errors for missing programs, or environment set ups. The end look like this: "config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands That is a normal finish. If i try to run "make" after this, it is compiling for some time until it stops with the following output: ": multiple definition of `fftwnd_f77_destroy_plan_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x680): first defined here /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x700): In function `fftwnd_f77_': : multiple definition of `fftwnd_f77_' My guess is that all of this gibberish is some kind of library/compiler unavailablity or incompatibility. You want to be sure you have loaded a compatible set of modules for the compiler and fftw library. I use modules intel-cc/9.0.031 and fftw/2.1.5-intel-9.0 and scsl/1.6.0.0 (the latter means you are using linear algebra stuff optimized for this machine instead of generic BLAS/LAPACK... not hugely important though) and for non-MPI have used ./configure --prefix=/home/224/mxa224/progs --with-fft=fftw2 --without-motif --with-external-blas --with-external-lapack CPPFLAGS=-I/opt/fftw-2.1.5/intel-9.0/include LDFLAGS='-L/opt/fftw-2.1.5/intel-9.0/lib/ -lscs' and for MPI have used ./configure --prefix=/home/224/mxa224/progs --with-fft=fftw2 --without-motif --with-external-blas --with-external-lapack CPPFLAGS=-I/opt/fftw-2.1.5/intel-9.0/include LDFLAGS='-L/opt/fftw-2.1.5/intel-9.0/lib/ -lscs -lmpi' --program-suffix=_mpi --enable-mpi all successfully. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS with MPICH on Sun Cluster
Alok wrote: Hi, I am trying to run GROMACS in parallel on a SUN Cluster with MPICH. I had installed FFTW 2.1.5 and Gromacs 3.2.1 without any error massage, but when i tried to use mdrun_mpi (or even mdrun_mpi -h) I got the following error message. how about mpirun mdrun -h [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_1870: p4_error: : 0 I followed the follwing procedure for installing FFTW 2.1.5 and GROMACS 3.2.1. First of all I set the PATH for MPICH files in my .profile file. PATH=/opt/mpichdefault-1.2.6/bin:$PATH PATH=/opt/mpichdefault-1.2.6/lib:$PATH PATH=/opt/mpichdefault-1.2.6/include:$PATH ### FFTW 2.1.5 # export MPICC=mpicc export LIBS="-lmpich -lfmpich -lpmpich" export MPILIBS="-L/opt/mpichdefault-1.2.6/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include" export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib" ./configure --enable-float --prefix=/users/bsbe/phd/alokjain/install/fftw --enable-mpi make make install # ## GROMACS 3.2.1 export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib -L/users/bsbe/phd/alokjain/install/fftw/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include -I/users/bsbe/phd/alokjain/install/fftw/include" ./configure --enable-mpi --prefix=/users/bsbe/phd/alokjain/install/gromacs --program-suffix=_mpi make make install # Any ideas regarding what is going wrong? Please let me know if you need more information... Thank you very much in advance, regards, Alok jain ___ 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] configuration, make, installation problem
Nevena Todorova wrote: Hi there, i am trying to install (double precision, mpi )Gromacs 3.3 on an SGI Altix system and during this process i encounter few problems. I configure the system using the commmand: ./configure --enable-mpi --enable-shared --disable-nice --disable-float --prefix=$HOME/g-3.3 --program-suffix=_d_mpi --with-fft=fftw2 and it seems to be running without problems untill the end where it stops without an output line for a successful configuration. It is not giving me an errors for missing programs, or environment set ups. The end look like this: "config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands " If i try to run "make" after this, it is compiling for some time until it stops with the following output: ": multiple definition of `fftwnd_f77_destroy_plan_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x680): first defined here /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x700): In function `fftwnd_f77_': : multiple definition of `fftwnd_f77_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x700): first defined here /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x780): In function `fftwnd_f77_one_': : multiple definition of `fftwnd_f77_one_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x780): first defined here ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook make[4]: *** [libgmx_mpi_d.la] Error 1 make[4]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/595/nxt595/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/595/nxt595/gromacs-3.3/src' make: *** [all-recursive] Error 1 " The installation guide on the Gromacs website is excellent, but i can not find a reason for these errors. I am new to Gromacs and i would appreciate it if anybody can help me out with this. How do i know if i have installed the programm successfully? Is there a conformation output in the very end, or is it a matter of testing it out??? Thanks in advance, Nevena ___ 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 check the link command line. are the fftw libraries included twice? a safe way is to do your own fftw libraries (use version 3 in that case). before doing anything else, do a make distclean, there could be leftovers from a single precision or non-mpi compilation -- 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] configuration, make, installation problem
Hi there, i am trying to install (double precision, mpi )Gromacs 3.3 on an SGI Altix system and during this process i encounter few problems. I configure the system using the commmand: ./configure --enable-mpi --enable-shared --disable-nice --disable-float --prefix=$HOME/g-3.3 --program-suffix=_d_mpi --with-fft=fftw2 and it seems to be running without problems untill the end where it stops without an output line for a successful configuration. It is not giving me an errors for missing programs, or environment set ups. The end look like this: "config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands " If i try to run "make" after this, it is compiling for some time until it stops with the following output: ": multiple definition of `fftwnd_f77_destroy_plan_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x680): first defined here /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x700): In function `fftwnd_f77_': : multiple definition of `fftwnd_f77_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x700): first defined here /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x780): In function `fftwnd_f77_one_': : multiple definition of `fftwnd_f77_one_' nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x780): first defined here ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook make[4]: *** [libgmx_mpi_d.la] Error 1 make[4]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/595/nxt595/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/595/nxt595/gromacs-3.3/src' make: *** [all-recursive] Error 1 " The installation guide on the Gromacs website is excellent, but i can not find a reason for these errors. I am new to Gromacs and i would appreciate it if anybody can help me out with this. How do i know if i have installed the programm successfully? Is there a conformation output in the very end, or is it a matter of testing it out??? Thanks in advance, Nevena ___ 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] Free volume: Pass and Gromacs
On Thu, 2006-06-08 at 15:14 +0200, Alessandro Mattozzi wrote: > Is it necessary to specify the atomtype in the index file or is it read from > the .gro file or the .tpr? Because i guess some data are needed (vdW radius) > to insert spheres in the free volume. > Thanx > Index files generally contain only atomic indexes and group names. As such, they only specify sets of atoms, and there is no way of specifying any additional information in the index file. See the manual for slightly more information. Atomtype, name and such stuff is as far as I know indeed read from the structure file (for example a tpr-file). The point of making an index file in this case is, I guess, that make_ndx creates a group consisting of the non-dummies. Erik Marklund Ph.D. Student ICM, Molecular biophysics Uppsala University Sweden > Alessandro Mattozzi > M.Phil., Ph.D. student > Dept. of Fibre and Polymer Technology > Royal Institute of Technology > Stockholm, Sweden > > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of David van der Spoel > Sent: Wed 6/7/2006 5:14 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Free volume: Pass and Gromacs > > Alessandro Mattozzi wrote: > > Hi all > > I wonder if anybody has been using Pass to measure free volume: I got > > these errors: > > > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > > Suggestion: Do I have to remove all the dummies? > Yes. > > make an index file, it will have a suitable group for it. > > > > > -Segmentation fault > > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > > some mistake in the conversion? > > > > Thanx > > > > 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 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] AFM Pulling Rate
Hello Bob, have you tried to define the initial position of the AFM-tip? It needs to be set to the position of the COM of the group you want to pull. try and add "afm_init1 = x y z" (x y z = position where the afm should be) to your pull.ppa. Otherwise your afmspring is extended from the beginning so much, that this extension dominates the force on the pulling group and the pullingrate is nearly irrelevant until the system relaxed. ciao Jan > Hello everyone, > I am using AFM pulling to drag a dna base across the surface of a graphene. > I'm > doing this in vaccuum. It seems that the base is pulled at the same rate no > matter what value I specify in afm_rate1. Here is my pull.ppa file: > > runtype = afm > group_1 = ssdna-ions > pulldim = N N Y > afm_rate1 = 0.05 > afm_k1 = 100 > afm_dir1 = 0 0 1 > > I'm using version 3.3. Does anyone know what's going on? > Thanks, > Bob Johnson > > ___ 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] Free volume: Pass and Gromacs
Is it necessary to specify the atomtype in the index file or is it read from the .gro file or the .tpr? Because i guess some data are needed (vdW radius) to insert spheres in the free volume. Thanx Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Wed 6/7/2006 5:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Free volume: Pass and Gromacs Alessandro Mattozzi wrote: > Hi all > I wonder if anybody has been using Pass to measure free volume: I got > these errors: > > -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. > Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a suitable group for it. > > -Segmentation fault > Suggestion: I use trjconv to get a pdb; is it possible that I am doing > some mistake in the conversion? > > Thanx > > 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 -- 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 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] Fatal error
Dear gmx-users: I am still learning how to use GROMACS and i would appreciate if someone could help me with this message error in Molecular Dynamics: Error on node 2, will try to stop all the nodes Halting parallel program mdrun on CPU 2 out of 6 --- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 220 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. I dont know what this means, does anyone know? Thanks in advance! Amanda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS with MPICH on Sun Cluster
Hi, I am trying to run GROMACS in parallel on a SUN Cluster with MPICH. I had installed FFTW 2.1.5 and Gromacs 3.2.1 without any error massage, but when i tried to use mdrun_mpi (or even mdrun_mpi -h) I got the following error message. [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_1870: p4_error: : 0 I followed the follwing procedure for installing FFTW 2.1.5 and GROMACS 3.2.1. First of all I set the PATH for MPICH files in my .profile file. PATH=/opt/mpichdefault-1.2.6/bin:$PATH PATH=/opt/mpichdefault-1.2.6/lib:$PATH PATH=/opt/mpichdefault-1.2.6/include:$PATH ### FFTW 2.1.5 # export MPICC=mpicc export LIBS="-lmpich -lfmpich -lpmpich" export MPILIBS="-L/opt/mpichdefault-1.2.6/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include" export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib" ./configure --enable-float --prefix=/users/bsbe/phd/alokjain/install/fftw --enable-mpi make make install # ## GROMACS 3.2.1 export LDFLAGS="-L/opt/mpichdefault-1.2.6/lib -L/users/bsbe/phd/alokjain/install/fftw/lib" export CPPFLAGS="-I/opt/mpichdefault-1.2.6/include -I/users/bsbe/phd/alokjain/install/fftw/include" ./configure --enable-mpi --prefix=/users/bsbe/phd/alokjain/install/gromacs --program-suffix=_mpi make make install # Any ideas regarding what is going wrong? Please let me know if you need more information... Thank you very much in advance, regards, Alok jain ___ 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
