Re: [gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6
Great -- if it doesn't seem to be working the way it should after some playing around, then submit it as a redmine issue, and I'll take a look. On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck jamb...@me.com wrote: Dear Michael, Thank you for your reply. Yes, it is relatively clear now. Will try to play around with this later today. Best, Joakim Date: Thu, 7 Mar 2013 08:55:31 -0500 From: Michael Shirts mrshi...@gmail.com Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella sampling with gmx 4.6 To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, Joakim- Hamiltonian exchange only should work if there is a lambda coupling parameter that defines the potential at each state. You need to define your pulling potential so that the coupling-lambda parameter can be used to define the different pulling location centers along your trajectory. Does this make it clearer? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_density fails after calculating for the last snapshot
Hi All I have a 100 ns lipid simulation for which I want the density profile. I issued the following command g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96] /usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec] /usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b] g_density(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d] g_density[0x400659] === Memory map: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f239000-7fb11f26c000 rw-p 00:00 0 7fb11f26c000-7fb11f282000 r-xp 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f483000-7fb11f485000 r-xp 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9d7000-7fb11f9df000 r--p 0015 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9e1000-7fb11f9e2000 rw-p 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd52000-7fb11fe4d000 r-xp 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004e000-7fb120066000 r-xp 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120066000-7fb120265000 ---p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120265000-7fb120266000 r--p 00017000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120267000-7fb12026b000 rw-p 00:00 0 7fb12026b000-7fb1204f9000 r-xp 08:06 4099651 /usr/lib/libgmx.so.6 7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206fe000-7fb120707000 rw-p 00293000 08:06 4099651 /usr/lib/libgmx.so.6 7fb120707000-7fb120708000 rw-p 00:00 0 7fb120708000-7fb1207f3000 r-xp 08:06 4099652 /usr/lib/libmd.so.6 7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f3000-7fb1209f4000
Re: [gmx-users] Use dihedraltype 4 to allow several multiplicity terms
Thank you all. I found that in my ffbonded.itp I had the same lines with other values. I used the new one produced by the newest version of paramchem blocking the old one. It works now. Steven On Thu, Mar 7, 2013 at 10:24 PM, Baptiste Demoulin bat.demou...@gmail.com wrote: Hello Steven, I would suggest you to look if this angle is not defined somewhere else in your file. Indeed, it seems that the program has another value for this. The 2 and 6 at the end of the line are the multiplicity, so they don't need to be changed. The relevant value is the one indicated in the 'func' column. 9 should be ok, since it describes a function of several Fourier term. I don't understand why grompp propose to chage this to 4... Baptiste 2013/3/7 Steven Neumann s.neuman...@gmail.com Dear Gmx Users, I used charmm server to get the parameters for my new molecule - alkane. i converted it into the gromacs topology. When I try grompp: WARNING 1 [file ffbonded.itp, line 7948]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159787 2 0 0.159787 2 new: CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 WARNING 2 [file ffbonded.itp, line 7949]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 0.159829 2 0 0.159829 2 new: CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 My ffnonbonded.itp corresponding lines: [ dihedraltypes ] ; i j k l funcphi0cp mult CG331 CG321 CG321 CG331 9 0.00 0.1598288 2 CG331 CG321 CG321 CG331 9 180.00 0.1330512 6 Can you please explain me this? Shall use 4 instead of 2 or 6 at the end of these lines? I am using Gromacs 4.5.5 Stevem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Special bonds with terminal residue
Thank you for your answer. I had tried to change the names before, but the error was then that the atoms were not recognized. Reading your answer made me realize that I had not gone far enough, The solution I found is to create a residue in the .rtp that has the same features as the terminal AA, but with a different name. Then, the fragment is renamed in the .pdb file according to this new residue (the atoms are renamed to), end the TER line is removed. I also added a block in .hdb file. And now it works well ! Thank you again ! Baptiste 2013/3/7 Justin Lemkul jalem...@vt.edu On 3/7/13 5:44 AM, Baptiste Demoulin wrote: Hello Gromacs users, I try to link a metallic core to its surrounding amino-acids. Everything works find for bonding side chains and metal atoms, but I have troubles when it comes to bonding COO- group from a terminus ALA. The error printed by pdb2gmx is the following : Program pdb2gmx, VERSION 4.6 Source code file: /home1/retegan/software/** gromacs-4.6/src/kernel/pgutil.**c, line: 126 Fatal error: Residue 334 named ALA of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type special bond in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Here my specbon.dat file : 22 CYS SG 1 CYS SG 1 0.2 CYS2CYS2 CYS SG 1 HEM FE 2 0.25CYS2HEME CYS SG 1 HEM CAB 1 0.18CYS2HEME CYS SG 1 HEM CAC 1 0.18CYS2HEME MET SD 1 HEM FE 1 0.24MET HEME CO C 1 HEMEFE 1 0.19CO HEME CYM SG 1 CYM SG 1 0.2 CYS2CYS2 HIS NE2 1 FE2 FE 4 0.23HID FE2 HIS NE2 1 OEX MN1 6 0.21HID OEX ASP OD2 1 OEX MN1 6 0.23ASP OEX GLU OE2 1 OEX MN1 6 0.20GLU OEX GLU OE1 1 OEX MN2 6 0.21GLU OEX ASP OD1 1 OEX MN2 6 0.21ASP OEX ALA OXT 1 OEX MN2 6 0.20ALA OEX GLU OE1 1 OEX MN3 6 0.21GLU OEX GLU OE2 1 OEX MN3 6 0.23GLU OEX SOX O 1 OEX MN4 6 0.21SOX OEX ASP OD2 1 OEX MN4 6 0.21ASP OEX GLU OE2 1 OEX MN4 6 0.22GLU OEX SOX O 1 OEX CA1 6 0.25SOX OEX ALA O 1 OEX CA1 6 0.25ALA OEX I tried to change the atom names within specbond.dat, in the initial pdb file, but nothing has worked yet... Does someone have an idea of what is going on ? Terminal oxygens are renamed according to the specifications in the relevant .c.tdb file. A terminal residue has no atom named O since the name is changed. If only one bond is missing, it's probably easiest to just manually add it to the topology, otherwise remove the offending line in specbond.dat, see how the terminal oxygens are renamed, and then try using the relevant atom name(s) for creating your bonds. If that approach doesn't work, then the only option is manual addition to the topology. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Thread affinity setting failed
Hi Reid, Just saw your bug report and realized that you have an ancient kernel which could be causing the issue. Let's move the discussion to the bug page ( http://redmine.gromacs.org/issues/1184), hopefully we can narrow the issue down and then post the conclusions to the list later. Cheers, -- Szilárd On Thu, Mar 7, 2013 at 7:06 AM, Roland Schulz rol...@utk.edu wrote: Hi Raid, I just tested Gromacs 4.6.1 compiled with ICC 13 and GCC 4.1.2 on CentOS 5.6 and I don't have any problems with pinning. So it might be useful to open a bug and provide more details, because it should work for CentOS 5.x. Yes, for pure water the group kernels are faster than Verlet. Roland On Wed, Mar 6, 2013 at 10:17 PM, Reid Van Lehn rvanl...@gmail.com wrote: Hi Szilárd, Thank you very much for the detailed write up. To answer your question, yes, I am using an old Linux distro, specifically CentOS 5.4, though upgrading to 5.9 still had the same problem. I have another few machines with different hardware CentOS 6.3 which does not have this issue so it is likely an operating system issue based on your description. As I'm (unfortunately...) also the sysadmin on this cluster I'm unlikely to find the time to upgrade all the nodes, so I'll probably stick with the -pin off workaround for now. Hopefully this thread might help out other users! As an aside, I found that the OpenMP + Verlet combination was slower for this particular system, but I suspect that it's because it's almost entirely water and hence probably benefits from the Group scheme optimizations for water described on the Gromacs website. Thanks again for the explanation, Reid On Mon, Mar 4, 2013 at 3:45 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi, There are some clarifications needed and as this might help you and other understand what's going on, I'll take the time to explain things. Affinity setting is a low-, operating system-level, operation and locks (=pins) threads to physical cores of the CPU preventing the OS from moving them which can cause performance drop - especially when using OpenMP-multithreading on multi-socket and NUMA machines. Now, mdrun will by default *try* to set affinity if you use all cores detected (i.e if mdrun can be sure that it is the only application running on the machine), but will by default *not* set thread affinities if the number of thread/processes per compute node is less than the number of cores detected. Hence, when you decrease -ntmpi to 7, you implicitly end up turning off thread pinning, that's why the warnings don't show up. The fact that affinity setting fails on your machine suggests that either the system libraries don't support this or the mdrun code is not fully compatible with your OS, the type of CPUs AFAIK don't matter at all. What OS are you using? Is it an old installation? If you are not using OpenMP - which btw you probably should with the Verlet scheme if you are running running on a single node or at high parallelization -, the performance will not be affected very much by the lack of thread pinning. While the warnings themselves can often be safely ignored, if only some of the threads/processes can't set affinities, this might indicate a problem. I your case, if you were really seeing only 5 cores being used with 3 warnings, this might suggest that while the affinity setting failed, three threads are using already busy cores overlapping with others which will cause severe performance drop. What you can do to avoid the performance drop is to turn of pinning by passing -pin off to mdrun. Without OpenMP this will typically not cause a large performance drop compared to having correct pinning and it will avoid the bad overlapping threads/processes case. I suspect that your machines might be running an old OS which could be causing the failed affinity setting. If that is the case, you should talk to your sysadmins and have them figure out the issue. If you have a moderately new OS, you should not be seeing such issues, so I suggest that you file a bug report with details like: OS + version + kernel version, pthread library version, standard C library version. Cheers, -- Szilárd On Mon, Mar 4, 2013 at 1:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Mar 4, 2013 at 6:02 AM, Reid Van Lehn rvanl...@mit.edu wrote: Hello users, I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to v 4.6. I'm using older 8 core Intel Xeon E5430 machines, and when I submitted a job for 8 cores to one of the nodes I received the following error: NOTE: In thread-MPI thread #3: Affinity setting failed. This can cause performance degradation! NOTE: In thread-MPI thread #2: Affinity setting
[gmx-users] QMMM installation with Cmake
Hi, I would like to report a problem when trying to install gromacs-4.6.1 with cmake together with QMMM orca interface. My installation command is as follows: CMAKE_INCLUDE_PATH=/opt/fftw/include CMAKE_LIBRARY_PATH=/opt/fftw/lib cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gmx-4.6.1_qmmm_orca -DGMX_QMMM_PROGRAM=ORCA -DGMX_PREFER_STATIC_LIBS=ON Although the GMX_QMMM_PROGRAM variable is properly set in CMakeCache.txt as GMX_QMMM_PROGRAM:STRING=ORCA it is not defined in src/config.h. I defined it by hand adding #define GMX_QMMM_ORCA in src/config.h. Everything is installed properly now and running. Maybe there is a way to correct for this in the cmake routine but I have no clue how to do that. Hope that helps also others who want to install with the same options. Regards, Esteban Vöhringer-Martinez Fac. Cs. Químicas, Universidad de Concepción, Chile -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_density fails after calculating for the last snapshot
What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also, can you extract that problematic frame with trjconv and run g_density on that one frame (what happens?). Also, can you make a new .xtc that is missing that last frame and see what g_density does? These will help you to figure out what is going on. Chris. -- original message -- Hi All I have a 100 ns lipid simulation for which I want the density profile. I issued the following command g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96] /usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec] /usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b] g_density(main+0x9)[0x400629] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d] g_density[0x400659] === Memory map: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb11f239000-7fb11f26c000 rw-p 00:00 0 7fb11f26c000-7fb11f282000 r-xp 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7fb11f483000-7fb11f485000 r-xp 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9d7000-7fb11f9df000 r--p 0015 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629 /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8 7fb11f9e1000-7fb11f9e2000 rw-p 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740 /usr/lib/libfftw3f.so.3.3.0 7fb11fd52000-7fb11fe4d000 r-xp 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916 /lib/x86_64-linux-gnu/libm-2.15.so 7fb12004e000-7fb120066000 r-xp 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120066000-7fb120265000 ---p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120265000-7fb120266000 r--p 00017000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910 /lib/x86_64-linux-gnu/libpthread-2.15.so 7fb120267000-7fb12026b000 rw-p 00:00 0 7fb12026b000-7fb1204f9000 r-xp 08:06 4099651 /usr/lib/libgmx.so.6 7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651 /usr/lib/libgmx.so.6 7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06
Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster
Hi Szilard Thanks for this tip; it was extremely useful. The problem was indeed the incompatibility between the installed NVIDIA driver and the CUDA 5.0 runtime library. Installation of an older driver solved the problem. The programs devideQuery etc can now detect the GPU. GROMACS can also detect now the card but unfortunately aborts with the following error Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 12 PP MPI processes per node, but only 1 GPU were detected. Here is my command line mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu What can be the problem? Thanks again Hi George, As I said before, that just means that most probably the GPU driver is not compatible with the CUDA runtime (libcudart) that you installed with the CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll have to do the research on that. Let us know if you have further (GROMACS-related) issues. Cheers, -- Szil?rd On Fri, Mar 1, 2013 at 2:48 PM, George Patargias g...@bioacademy.gr wrote: Hi Szilαrd Thanks for your reply. I have run the deviceQuery utility and what I got back is /deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected Should I understand from this that the CUDA driver was not installed from the MAC OS X CUDA 5.0 Production Release? George HI, That looks like the driver does not work or is incompatible with the runtime. Please get the SDK, compile a simple program, e.g. deviceQuery and see if that works (I suspect that it won't). Regarding your machines, just FYI, the Quadro 4000 is a pretty slow card (somewhat slower than a GTX 460) so you'll hava a quite strong resource imbalance: a lot of CPU compute power (2x Xeon 5xxx, right?) and little GPU compute power which will lead to the CPU idling while waiting for the GPU. Cheers, -- Szilαrd On Thu, Feb 28, 2013 at 4:52 PM, George Patargias g...@bioacademy.grwrote: Hello We are trying to install the GPU version of GROMACS 4.6 on our own MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro 4000 cards: - We have downloaded and install the MAC OS X CUDA 5.0 Production Release from here: https://developer.nvidia.com/cuda-downloads placing the libraries contained in this download in /usr/local/cuda/lib - We have managed to compile GROMACS 4.6 linking it statically with these CUDA libraries and the MPI libraries (with BUILD_SHARED_LIBS=OFF and GMX_PREFER_STATIC_LIBS=ON) Unfortunately, when we tried to run a test job with the generated mdrun_mpi, GROMACS reported that it cannot detect any CUDA-enabled devices. It also reports 0.0 version for CUDA driver and runtime. Is the actual CUDA driver missing from the MAC OS X CUDA 5.0 Production Release that we installed? Do we need to install it from here: http://www.nvidia.com/object/cuda-mac-driver.html Or is something else that we need to do? Many thanks in advance. George Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. *
[gmx-users] query regarding mk_angndx
Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -type dihedral output angle.ndx read like this - [ Phi=180.0_2_43.93 ] 52018192237353627323031 395957586176747566716970 ... According to my understanding the numbers indicate the 4 atoms defining the particular dihedral angle. But when I checked the pdb file for these atoms- ATOM 5 CA MET A 1 111.430 40.170 113.130 1.00 0.00 ATOM 18 C MET A 1 112.060 41.020 112.030 1.00 0.00 ATOM 19 O MET A 1 111.910 42.240 112.010 1.00 0.00 ATOM 20 N GLN A 2 112.940 40.430 111.220 1.00 0.00 I could not make out how this defines phi? Kindly clarify my confusion. Thank you kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dihre_fc option in new 4.6.1 version
Dear users, I want to apply dihedral restraint and got everything set up in the topology but I do not know the way to define the restraining force constant. In the older grimaces versions one had the dihre_fc option but this is not present in the 4.6 version. I read a post on the user list about a change in the dihedral restrain part of the code to equal it to the free energy code by Michael Skirts but nothing about the way to define the force constant. Also the manual does not have this information. I would appreciate any help on this. Thanks in advance, Esteban Vöhringer-Martinez, Fac. Cs. Químicas, Universidad de Concepción, Chile-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs with Intel Xeon Phi coprocessors ?
Dear users: does anybody have any experience with gromacs on a cluster in which each node is composed of 1 or 2 x86 processors plus an Intel Xeon Phi coprocessor? Can gromacs make use of the xeon phi coprocessor? If not, does anybody know if that is in the pipeline? Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: RDF for INVACCUO simulation
DEAR ALL For RDF calculation in invaccuo simulation I have given the command as follows ./g_rdf_d -f outputdsvaccum_md.trr -s outputdsvaccum_md.tpr -n index.ndx -nopbc -o rdfss.xvg I am getting the graph which I have attached with this mail. Can you suggest whether my command and the graph is correct and I am proceeding in the right way. Thanks in Advance with regards Keerthana.S.P -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Performance of 4.6.1 vs. 4.5.5
Dear users: I am seeing a 140% performance boost when moving from gromacs 4.5.5 to 4.6.1 when I run a simulation on a single node. However, I am only seeing a 110% performance boost when running on multiple nodes. Does anyone else see this? Note that I am not using the verlet cutoff scheme. I'm not sure that this is a problem, but I was surprised to see how big the difference was between 1 and 2 nodes, while for 2-10 nodes I saw a reliable 10% performance boost. Please note that, while I compiled the fftw (with sse2) and gromacs 4.6.1, I did not compile the 4.5.5 version that I am comparing to (or its fftw) so the difference might be in compilation options. Still, I wonder why the benefits of 4.6.1 are so fantastic on 1 node but fall off to good-but-not-amazing on 1 node. The system is about 43K atoms. I have not tested this with other systems or cutoffs. My mdp file follows. Thank you for any advice. Chris. constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nsteps = 25 nstcomm = 1 nstxout = 25 nstvout = 25 nstfout = 25 nstxtcout = 5 nstenergy = 5 nstlist = 10 nstlog=0 ns_type = grid vdwtype = switch rlist = 1.0 rlistlong = 1.6 rvdw = 1.5 rvdw-switch = 1.4 rcoulomb = 1.0 coulombtype = PME ewald-rtol = 1e-5 optimize_fft = yes fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 310 gen_temp = 310 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 4 4 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 dispcorr = EnerPres -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
