[gmx-users] how to calculate kinetic constant?
Hello: I've submit a simulation in gromacs, and I am just wondering how can we calculate kinetic constant for the ligand bound/ubound process? thanks a lot Albert -- 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] g_select problem
On 09/28/2013 09:42 AM, rajat desikan wrote: Hi, I am not sure, but try resname SOL or something similar. Also, your first line has waterO and second line has water0. Hi Rajat: thanks a lot for such kind and helpful comments. It works now. I run it by command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat -os size.xvg -oc cfrac.xvg -oi index.dat I am trying to make density of the water molecules inside my protein by g_density: g_density_mpi -f ../md_pbc_center.xtc -s ../md.tpr -ei density.ndx -o density.xvg -n density.ndx but it asked me which water molecules I would like to make. Do you have any idea how to do this correctly? thank you very much. best Albert -- 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_select problem
Hello: I am trying to analyze the water density along Z direction of my protein. Here is my g_select command: g_select_mpi -f ../md_pbc_center.xtc -s ../md.tpr -on density.ndx -sf select.dat and here is my select.dat: waterO = water and name OW and z>30 and z<70; close = water0 and within 0.4 of group Protein; close it failed with messages: Reading file ../md.tpr, VERSION 4.6.3 (single precision) Reading file ../md.tpr, VERSION 4.6.3 (single precision) selection parser: syntax error selection parser: invalid selection 'waterO = water and name OW and z>30 and z<70' I am just wondering, is there anything wrong with my syntax? thank you very much. best Albert -- 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] identical results or exactly the same results?
Hello: I've got a md.tpr file generated by grompp, I am just wondering will the results be identical or would be exactly the same if I run it in different machine? thank you very much. best Albert -- 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] is there any tool for flexibility?
On 09/01/2013 06:03 PM, Justin Lemkul wrote: Maybe g_msd or g_rmsf, but I don't think there's anything specifically designed to address water molecules, and the term "flexibility" can have far too many meanings ;) -Justin thanks a lot for kind messages. but there are a lot of water molecules in those region. Moreover, those water molecules can exchange with bulk environment. In this case, it would be very difficult to use g_msd or g_rmsf for this purpose. I don't know which tool or which method would be good to describe this observation... -- 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] is there any tool for flexibility?
Hello: I've finished a MD with Gromacs and I found that the water molecules inside certain region of my protein is very flexible: the movement of them are very fast; in other region there are very stable. I am just wondering is there any tool in Gromacs can differentiate the water molecules' flexibility? thank you very much best Albert -- 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] efficiency in HPC
On 08/29/2013 10:31 PM, Prentice Bisbal wrote: Albert, It looks like you are trying to compile for an IBM Power 7 system. What is the 'other machine' you are comparing it to, and did you use the same number of cores in each case? Prentice yes it is. here is the configurations: * 4 IBM POWER7 processors; detailed configuration: o architecture ppc64 (specification Power ISA v.2.06) o 64 bit o 8 cores o core clock rate 3.83 Ghz o up to 4 SMT threads per core o 64 kB (32 kB instructions + 32 kB data) cache L1 per core o 256 kB cache L2 per core o 4 MB cache L3 per core * SMP * 32 cores * 128 GB RAM * theor. peak perf. 980 GFlops/s * dedicated operating system AIX 7.1 I compared with the following one, obviously the following one hardware is poor than above one but efficiency is much better. There must be something wrong with the compiling AMD Quad-Core Opteron 835X nodes x86_64 architecure 432 nodes 16 cores each 16/32 GB per node for memobry THX Albert -- 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] efficiency in HPC
Hello: I compiled 4.6.3 in HPC with following steps: setenv OBJECT_MODE 64 /opt/cmake/2.8.9_new/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs/4.6.3 -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Release -DGMX_SOFTWARE_INVSQRT=OFF -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI =OFF -DGMX_X11=OFF -DGMX_FLOAT_FORMAT_IEEE754=1 -DGMX_IEEE754_BIG_ENDIAN_BYTE_ORDER=1 -DGMX_IEEE754_BIG_ENDIAN_WORD_ORDER=1 -DCMAKE_C_COMPILER="/usr/bin/mpcc_r" -DCMAKE_CXX_COMPILER="/usr/bin/mpCC_ r" -DCMAKE_C_FLAGS_RELEASE="-O3 -qstrict -qsimd=auto -qmaxmem=-1 -qarch=pwr7 -qtune=pwr7" -DCMAKE_XX_FLAGS_RELEASE="-O3 -qstrict -qsimd=auto -qmaxmem=-1 -qarch=pwr7 -qtune=pwr7" -DFFTWF_LIBRARY="/o pt/fftw/3.3.2/lib/libfftw3f.a" -DFFTWF_INCLUDE_DIR="/opt/fftw/3.3.2/include" -DCMAKE_LINKER="/usr/bin/mpcc_r" gmake -j 16 gmake install when I do the test, I found that the performance is really bad. It tooks more than one year for a job to be done while it only take 2 months in other machine. Does anybody have any idea where is the problem? thanks a lot Albert -- 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] problem of submitting job in HPC
hello Mark: thanks a lot for kind advices. Here is my log file for output of mdrun -version, There are always some duplicate informations and files Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Program: mdrun_mpi Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:(1.0/__sqrt(x)) CPU acceleration: NONE FFT library:fftw-3.3.2-fma Large file support: enabled RDTSCP usage: disabled Built on: Thu Aug 29 02:03:12 CEST 2013 Built by: sheed@c2n25-hf0 [CMAKE] Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:(1.0/__sqrt(x)) CPU acceleration: NONE FFT library:fftw-3.3.2-fma Large file support: enabled RDTSCP usage: disabled Built on: Thu Aug 29 02:03:12 CEST 2013 Built by: sheed@c2n25-hf0 [CMAKE] Build OS/arch: AIX 1 00CCE0564C00 Build CPU vendor: Unknown Build CPU brand:Unknown CPU brand Build CPU family: 0 Model: 0 Stepping: 0 Build CPU features: CannotDetect C compiler: /usr/bin/mpcc_r XL mpcc_r C compiler flags: -qlanglvl=extc99 -qarch=auto -qtune=auto -qthreaded -qalias=noansi -qhalt=e -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa rch=pwr7 -qtune=pwr7 Build OS/arch: AIX 1 00CCE0564C00 Build CPU vendor: Unknown Build CPU brand:Unknown CPU brand Build CPU family: 0 Model: 0 Stepping: 0 Build CPU features: CannotDetect C compiler: /usr/bin/mpcc_r XL mpcc_r C compiler flags: -qlanglvl=extc99 -qarch=auto -qtune=auto -qthreaded -qalias=noansi -qhalt=e -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa rch=pwr7 -qtune=pwr7 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:(1.0/__sqrt(x)) CPU acceleration: NONE FFT library:fftw-3.3.2-fma Large file support: enabled RDTSCP usage: disabled Built on: Thu Aug 29 02:03:12 CEST 2013 Built by: sheed@c2n25-hf0 [CMAKE] Build OS/arch: AIX 1 00CCE0564C00 Build CPU vendor: Unknown Build CPU brand:Unknown CPU brand Build CPU family: 0 Model: 0 Stepping: 0 Build CPU features: CannotDetect C compiler: /usr/bin/mpcc_r XL mpcc_r C compiler flags: -qlanglvl=extc99 -qarch=auto -qtune=auto -qthreaded -qalias=noansi -qhalt=e -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa rch=pwr7 -qtune=pwr7 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:(1.0/__sqrt(x)) CPU acceleration: NONE FFT library:fftw-3.3.2-fma Large file support: enabled RDTSCP usage: disabled Built on: Thu Aug 29 02:03:12 CEST 2013 Built by: sheed@c2n25-hf0 [CMAKE] Build OS/arch: AIX 1 00CCE0564C00 Build CPU vendor: Unknown Build CPU brand:Unknown CPU brand Build CPU family: 0 Model: 0 Stepping: 0 Build CPU features: CannotDetect C compiler: /usr/bin/mpcc_r XL mpcc_r C compiler flags: -qlanglvl=extc99 -qarch=auto -qtune=auto -qthreaded -qalias=noansi -qhalt=e -O3 -qstrict -qsimd=auto -qmaxmem=-1 -qa rch=pwr7 -qtune=pwr7 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:MPI . . . 2013/8/28 Mark Abraham > On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul wrote: > > > > > > On 8/28/13 12:39 PM, Albert wrote: > >> > >> Hello: > >> > >> I am trying to use following command to run 4.6.3 in a HPC cluster: > >> > >> mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x > >> md.xtc > >> -o md.trr -g md.log -e md.edr >& md.info > >> > >> the 4.5.5 works fine in this machine with command: > >> > >> mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g > >> md.log > >> -e md.edr >& md.info > >> > >> the difference is that the option "-nosum" is not available in 4.6.3 > >> > >> but 4.6.3 always failed. It generate a lot of similar files and log > >>
Re: [gmx-users] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:38 PM, Justin Lemkul wrote: That's not the problem. It's complaining about whatever is on line 1 (not clear from the previous message if the comment line is #1 or a blank line), so assuming that the #ifdef is in the right place (probably is, or the error would be different), it's possible that there's some weird hidden character that is causing the error. -Justin IC. the problem solved when I run command dos2unix. thank you very much. Albert -- 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] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:25 PM, Justin Lemkul wrote: Looks normal, so without context of how it is #included, there's not much to diagnose here. here is my #include in topol.top file: ; Include Position restraint file #ifdef POSRES #include "restrain.itp" #endif I first generate restrain for all the protein CA by genrest command, after that I delete the atoms which I don't want to restrain from output restrain.itp. Probably that's the problem? Maybe I should set the unwanted restrain atoms into 0 force constant instead of delete them from restrain.itp file? thx a lot Albert -- 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] work in 4.5.5 but failed in 4.6.1
On 08/28/2013 07:07 PM, Justin Lemkul wrote: WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) Looks concerning - what's line 1? here is the initial lines: ; position restraints for part of C-alpha of Protein [ position_restraints ] ; i funct fcxfcyfcz 51300300300 241300300300 WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) How big is your box? This may very well be a simple periodicity issue. http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb -Justin I've see this informations from gromacs website. my box is: 6.96418 6.96418 9.77176 in the last line of my input .gro file. I don't understand, why this warning not appear in 4.6.3, but failed in 4.5.5 thank you very much Albert -- 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] problem of submitting job in HPC
Hello: I am trying to use following command to run 4.6.3 in a HPC cluster: mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr >& md.info the 4.5.5 works fine in this machine with command: mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr >& md.info the difference is that the option "-nosum" is not available in 4.6.3 but 4.6.3 always failed. It generate a lot of similar files and log informations. It looks like use mpiexec evoke serial mdrun. Does anybody have any idea? thank you very much. best Albert -- 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] work in 4.5.5 but failed in 4.6.1
Hello: I am constraining one part of the protein and trying to generate md.tpr with command: grompp -f md.mdp -c npt4.gro -n -o md.tpr it works fine in 4.6.3, but it failed in 4.5.5 with following warning messages: WARNING 1 [file md.mdp, line 65]: Unknown left-hand 'cutoff-scheme' in parameter file WARNING 2 [file helix.itp, line 1]: Too few parameters on line (source file toppush.c, line 1501) WARNING 3 [file md.mdp]: The sum of the two largest charge group radii (13.715767) is larger than rlist (1.00) There were 3 notes There were 3 warnings --- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1584 Does anybody have any idea? thx Albert -- 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] g_select problem
On 08/21/2013 05:06 PM, Justin Lemkul wrote: Your selection, as Teemu says, is calling for *atoms* named T3P that are also *atoms* named O, which is clearly impossible. The *residue* name is T3P. -Justin I see. thanks a lot for clearly pointing out. I changed it into resname T3P and it works very well now. thanks all you guys. best Albert -- 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] g_select problem
but actually the water name in my system IS "T3P" and the atom name in the water model is "O". I've double checked for this. thx Albert On 08/21/2013 04:59 PM, Teemu Murtola wrote: If that is really your selection, you are trying to select atoms that have both name T3P and O, which is clearly impossible, so nothing gets selected. Best regards, Teemu -- 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] g_select problem
Hello Mark: thanks for kind advices. I checked my residues number carefully, and I didn't find anything wrong. However, I am not sure whether the syntax of my selection.dat is all right or not, since the documentation for this option is not well clarified. thank you very much Albert On 08/21/2013 04:35 PM, Mark Abraham wrote: Simplify your condition gradually and find out which bit is wrong! Mark -- 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_select problem
Hello: I am trying to calculate the number of water molecules within 3 A of a resid 51, and here is my command: g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat here is my selection.dat: waterO = name "T3P" and name O; close = waterO and within 0.3 of resnr 51; close the command run without errors, but I noticed that the number of water molecules in the output file are all 0. When I visualize each frame, I observe a lot of water molecules within the defined region. Does anybody have any idea what's the problem? thx Albert -- 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] itp problem
Hello: I am trying to restrain part of my protein. First I generate a index file by make_ndx. Then I use genrest for this purpose like: genres -f npt.gro -o helix -n -fc 400 after that I change the following in the topol.top file, like: ; Include Position restraint file #ifdef POSRES #include "helix.itp" #endif when I run grompp, it claimed following warnings: WARNING 1 [file helix.itp, line 1]: Too few parameters on line (source file /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 1756) here is my helix.itp: ; position restraints for System of [ position_restraints ] ; i funct fcxfcyfcz 51400400400 241400400400 411400400400 481400400400 591400400400 701400400400 861400400400 1071400400400 1261400400400 1401400400400 1561400400400 1711400400400 1901400400400 2001400400400 2191400400400 2291400400400 2451400400400 2641400400400 2741400400400 thank you very much. Albert -- 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] GPU metadynamics
On 08/15/2013 11:21 AM, Jacopo Sgrignani wrote: Dear Albert to run parallel jobs on multiple GPUs you should use something like this: mpirun -np (number of parallel sessions on CPU) mdrun_mpi .. -gpu_id so you will have 4 calculations for GPU. Jacopo thanks a lot for reply. but there is some problem with following command: mpirun -np 4 mdrun_mpi -s md.tpr -v -g md.log -o md.trr -x md.xtc -plumed plumed2.dat -e md.edr -gpu_id 0123. --log--- 4 GPUs detected on host node3: #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/albert/install/source/gromacs-4.6.3/src/gmxlib/gmx_detect_hardware.c, line: 349 Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 1 PP MPI process per node, but you provided 4 GPUs. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] GPU metadynamics
Hello: I've got two GTX690 GPU in a workstation, and I compiled gromacs-4.6.3 with plumed and MPI support. I am trying to run some metadynamics with mdrun with command: mdrun_mpi -s md.tpr -v -g md.log -o md.trr -x md.xtc -plumed plumed2.dat -e md.edr but mdrun can only use 1 GPU as indicated in the log file: 4 GPUs detected on host node3: #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible NOTE: potentially sub-optimal launch configuration, mdrun_mpi started with less PP MPI process per node than GPUs available. Each PP MPI process can use only one GPU, 1 GPUs per node will be used. 1 GPU auto-selected for this run: #0 I am just wondering how can we use multiple GPU for such kind of jobs? THX Albert -- 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] how can we control output ?
Hello: I am producing MD production with command: mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o md.trr -e md.edr I notice that it generate two additional files: HILLS COLVAR the output in this two files are very frequent such as: #! FIELDS time cv1 cv2 vbias 0. -1.372322679 0.4671409730.0 0.0900 -1.225425363 0.4868991370.02999 0.1800 -1.420091748 0.5462185740.031921782 0.2700 -1.430565715 0.5849254130.057605527 0.3600 -1.193568826 0.5248758790.056731977 0.4500 -1.215992570 0.4391220810.074018419 0.5400 -1.320514202 0.3950026330.059704699 0.6300 -1.247566938 0.4936060310.119831786 0.7200 -1.258976460 0.4036847650.120678633 AND: 0.090 -1.225425363 0.486899137 0.08697 0.08697 0.061249998 1.960 0.180 -1.420091748 0.546218574 0.08697 0.08697 0.061201861 1.960 0.270 -1.430565715 0.584925413 0.08697 0.08697 0.060562217 1.960 0.360 -1.193568826 0.524875879 0.08697 0.08697 0.060583858 1.960 0.450 -1.215992570 0.439122081 0.08697 0.08697 0.060157006 1.960 0.540 -1.320514202 0.395002633 0.08697 0.08697 0.060510237 1.960 0.630 -1.247566938 0.493606031 0.08697 0.08697 0.059040397 1.960 0.720 -1.258976460 0.403684765 0.08697 0.08697 0.059019958 1.960 0.810 -1.331293344 0.531644762 0.08697 0.08697 0.059053400 1.960 0.900 -1.477816820 0.541284800 0.08697 0.08697 0.059861982 1.960 I am performing 200 ns MD simulations. The file probably will become too big I am just wondering how can we setup the frequency record for the HILL and COLVAR file? THX Albert -- 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] Re: Unkwown Keyword HILLS
On 08/14/2013 12:26 PM, Michael Shirts wrote: This is a plumed error, not a gromacs error. Gromacs never handles those keywords. Sent from my iPhone IC THX, it works now. I found some "strange characters" in the plumed.dat file. After delete them, it work now -- 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: Unkwown Keyword HILLS
Does anybody have any idea what's the problem? I use the tutorial example and I don't know why it doesn't work. THX On 08/13/2013 07:19 PM, Albert wrote: Dear: I am trying to run plumed with gromacs plugin. Here is my plumed.dat file which I defined two dihedral angels as cvs: *HILLS HEIGHT 0.3 W_STRIDE 450 WELLTEMPERED SIMTEMP 310 BIASFACTOR 1.96 TORSION LIST 1 4 65 344 SIGMA 0.12 TORSION LIST 2 46 80 656 SIGMA 0.12 ENDMETA* I am using plumed-1.3+gromacs-4.6.2 with command: *mpirun -np 24 mdrun_mpi -s md.tpr -plumed plumed.dat -g md.log -v -x md.xtc -o md.trr -e md.edr* but it failed with messages: *starting mdrun 'protein' 1 steps, 20.0 ps. ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS ! ABORTING RUN ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS ! ABORTING RUN --* thank you very much Albert -- 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] Unkwown Keyword HILLS
Dear: I am trying to run plumed with gromacs plugin. Here is my plumed.dat file which I defined two dihedral angels as cvs: *HILLS HEIGHT 0.3 W_STRIDE 450 WELLTEMPERED SIMTEMP 310 BIASFACTOR 1.96 TORSION LIST 1 4 65 344 SIGMA 0.12 TORSION LIST 2 46 80 656 SIGMA 0.12 ENDMETA* I am using plumed-1.3+gromacs-4.6.2 with command: *mpirun -np 24 mdrun_mpi -s md.tpr -plumed plumed.dat -g md.log -v -x md.xtc -o md.trr -e md.edr* but it failed with messages: *starting mdrun 'protein' 1 steps, 20.0 ps. ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS ! ABORTING RUN ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS ! ABORTING RUN --* thank you very much Albert -- 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] Re: problem in g_membed
superimpose your receptor PDB files with related structure OPM database center your lipids in 0 by editconf command in gromacs then you GPCR would be in the center of the lipids. PS: 340 lipids is too big for a single GPCR, 140~160 would be enough before g_membed. You'd better read paper to see how many lipids did other people use. On 07/29/2013 10:31 AM, pavithrakb wrote: Thank you both of you (Justin and Albert) sir. Initially I was using dppc128 and now I changed to POPE 340 and still my protein (its a GPCR protein) protrude out of the membrane (the same region; two amino acids). since you (Justin) you have mentioned that the protein must be completely inside the membrane to avoid any instability, what must I do to avoid this problem? is something wrong with my protein? The region protruding out is a loop. is it still a problem? the protein's box size is 4.49101 4.74797 7.29103 (from protein.gro). Kindly help. -- 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] binding energy for membrane system
Hello: I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI and so on) website for binding energy evaluation are all for protein in water. I am just wondering how can we evaluate the protein/ligand binding affinity for membrane system accurately? Probably the most difficult thing is to evaluate the term from protein/lipids and protein/water part, since the system is heterogeneous instead of homogeneous. thank you very much. Albert -- 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] How to calculate enthalpy
On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote: Sure, you can. Dr. Vitaly V. Chaban I've got a question for it. Why the calculated entropy is negative? -- 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] a question on energygrps
Hello: I've got a question on energygrps options in .mdp file. This option is usually used for establishing the groups for the energy output. I am going to study the entropy changes of protein-ligand-SOL in a membrane system, I am just wondering shall I specify each compoenent in energygrps option, like: energygrps = Protein LIG SOL POPC I am also going to use g_lie for interaction analysis, will the above options be sufficient? If I forgot to assign the energygrps options in my md.mdp file during MD simulations, is it any fast way to calculate the energy after MD instead of running the simulation from beginning? I notice that there is a tool called g_lie can be used to evaluate protein/ligand binding, I am just wondering is there any paper on this tool? I don't find too much informations on gromacs manual. thank you very much Albert -- 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] why DGbind=0 ?
Hello: I am using glie to evaluate my ligand binding affinity with command: g_lie_d -f md.edr -o lie.xvg -ligand LIG but I obtained the following results: Opened md.edr as single precision energy file Using the following energy terms: LJ: Coul: DGbind = 0.000 (0.000) @title "LIE free energy estimate" @xaxis label "Time (ps)" @yaxis label "DGbind (kJ/mol)" @TYPE xy 0 0 1000 0 2000 0 3000 0 4000 0 5000 0 6000 0 7000 0 8000 0 9000 0 1 0 11000 0 12000 0 13000 0 14000 0 15000 0 16000 0 17000 0 18000 0 19000 0 2 0 21000 0 22000 0 23000 0 24000 0 I am just wondering why the result is zero? thank you very much Albert -- 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] cuda problem
On 07/09/2013 11:15 AM, Szilárd Páll wrote: Tesla C1060 is not compatible - which should be shown in the log and standard output. Cheers, -- Szilárd THX for kind comments. do you mean C1060 is not compatible with cuda-5.0 toolkit? or it is not compatable with Gromacs-4.6.3?I only obtained the following information in the log file 2 GPUs detected on host c0107: #0: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible #1: NVIDIA Tesla C2075, compute cap.: 2.0, ECC: yes, stat: compatible 2 GPUs auto-selected for this run: #0, #1 NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known to cause performance loss. Switching to the alternative polling GPU wait. If you encounter issues, switch back to standard GPU waiting by setting the GMX_CUDA_STREAMSYNC environment variable. Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity best Albert -- 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] cuda problem
Dear: I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the following information for testing: NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known to cause performance loss. Switching to the alternative polling GPU wait. If you encounter issues, switch back to standard GPU waiting by setting the GMX_CUDA_STREAMSYNC environment variable. The cuda version in the GPU cluster is 4.2 and the GPU is: Tesla C1060 I notice that the performanc is really slow. I am just wondering how can we solve this problem? which directory should I set up for GMX_CUDA_STREAMSYNC? THX Albert -- 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] Re: problem in g_membed
Just a piece of advices: you can consider equilibrate a lipids system which is large enough for your protein. This will save you huge amount of time on using tricks to add water later or enlarge the lipids. The system MUST BE IN PBC BOX for the g_membed input coordinate, otherwise your job would be failed in the following step. You can visualize your system in VMD to double check. If it is not in the PBC BOX, you can use editconf -box to fix this issue. good luck. Albert On 07/08/2013 11:40 AM, Justin Lemkul wrote: On 7/7/13 10:52 PM, pavithrakb wrote: Dear Sir, Thanks so much.. now what's the solution? Should I increase the box size? Yes. If the protein protrudes "out" of the central image, then you will have an unstable system due to atomic overlap as well as violations of the minimum image convention. Already I have centered the protein and fixed the POPE membrane size. Can you tell me how to increase the box size? or is there any other solution? If you need more space in the x-y plane, use genconf to replicate the membrane patch appropriately. If x-y is sufficient and only z is the problem, use editconf to adjust the box size and (if desired) the location of the membrane-protein complex and then solvate with genbox to fill the newly introduced void. -Justin -- 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] why TIPS3P, why not TIP3P?
On 07/08/2013 10:47 AM, Javier Cerezo wrote: In a recent benchmark by Piggot, Piñeiro and Khalid ( http://pubs.acs.org/doi/abs/10.1021/ct3003157 ), they showed that the TIP3P flavour may affect some properties (ApL) for simulations with CHARM36, concluding that CHARMM-TIP3P is recommended, at least for DPPC. I've also experienced similar issues with DMPC. Javier which CHARMM36 FF do you use? The CHARMM36 is being update from time to time. It may have some influence on the head property of the lipids, but how much it would be for the whole protein/membrane system, it is still unclear. For the long time scaled MD simulations, many people would be hesitated to introducing charmm-TIP3P which sacrifice too much speed. I've also observed that in several paper, people said Na+ have influence on POPC property similar to your claims, but most people still prefer to use POPC+0.15M NaCl which is the most close system to physiology environment. Albert -- 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] why TIPS3P, why not TIP3P?
Hello: I noticed that the CHARMM36 FF recommend CHARMM TIP 3-point with LJ on H's model for lipids when we run pb2gmx each time. I am just wondering, why it is recommend for lipids? Is there any special superior reason to do so? As far as I google both Gromacs maillist and CHARMM forum, most people conclude that there is no big differences between CHARMM TIP3 model and original TIP3P model. Here is what I found: http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23727 http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23422#Post23422 http://pubs.acs.org/doi/full/10.1021/ct900549r http://lists.gromacs.org/pipermail/gmx-users/2010-September/053966.html Actually, in one of the recent De.Shaw CELL paper (http://www.sciencedirect.com/science/article/pii/S0092867412015528), they also introduced normal TIP3P water model+ CHARMM36 FF for their system. In this work, they performed 100+ us long time scaled MD simulation for a extremely large membrane protein. could anybody comment on this issue? THX a lot. Albert -- 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] 11-cis retinal topology problem
On 07/07/2013 10:23 AM, Mark Abraham wrote: The error happens on the last line it reached. Take a look at it:-) Mark Hi Mark: thanks again for kind helps these days. My problem solved now: my original charmm file was mixed with old parameters which I worked on before. After I start from a fresh file, everything goes well now. best regards Albert -- 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] 11-cis retinal topology problem
On 07/07/2013 10:23 AM, Mark Abraham wrote: Program grompp, VERSION 4.6.3 >Source code file: >kernel/topdirs.c, line: 106 > Hello Mark: thanks a lot for kind reply. Do you mean the above information? I open this file and here is the line 106: gmx_fatal(FARGS, "Invalid angle type %d", type); here is the angetypes section in the ffbonded.itp file which generated from the python scrips, to be honest I don't see anything bad thank you very much. Albert [ angletypes ] ; ijkfuncth0cthub0cub CT2CT2NCH15111.20669.440.00.0 HCRNCH1CT25118.40292.880.00.0 CT2NCH1CR155123.20418.40.00.0 CR15NCH1HCR5120.00292.880.00.0 HACT2NCH15109.50418.40.00.0 NCH1CR15HPL15119.10292.880.00.0 NCH1CR15CR145122.90794.960.00.0 CR15CR14HPL5119.70292.880.00.0 CR14CR15HPL15119.70292.880.00.0 CR15CR14CR135122.90794.960.00.0 CR14CR13CT35119.70585.760.00.0 CR13CR14HPL5119.70292.880.00.0 CR13CT3HA5109.50418.40.00.0 CR14CR13CR125122.90794.960.00.0 CR13CR12HPL5119.70292.880.00.0 CR12CR13CT35119.70585.760.00.0 CR13CR12CR115122.90794.960.00.0 CR12CR11HPL5119.70292.880.00.0 CR11CR12HPL5119.70292.880.00.0 CR12CR11CR105122.90794.960.00.0 CR11CR10HPL5119.70292.880.00.0 CR10CR11HPL5119.70292.880.00.0 CR11CR10CR95122.90794.960.00.0 CR10CR9CT35119.70585.760.00.0 CR9CT3HA5109.50418.40.00.0 CR9CR10HPL5119.70292.880.00.0 CR10CR9CR85122.90794.960.00.0 CR9CR8HPL5119.70292.880.00.0 CR8CR9CT35119.70585.760.00.0 CR9CR8CR75122.90794.960.00.0 CR8CR7HPL5119.70292.880.00.0 CR7CR8HPL5119.70292.880.00.0 CR8CR7CR65122.90794.960.00.0 CR7CR6CT35119.70585.760.00.0 CR6CR7HPL5119.70292.880.00.0 CR7CR6CR55122.90794.960.00.0 CR6CR5CT35119.70585.760.00.0 CR6CR5CT25119.70585.760.00.0 CT3CR5CT25119.70585.760.00.0 CR5CT2HA5109.50418.40.00.0 CR5CT3HA5109.50418.40.00.0 CR6CT3CT25111.10527.1840.00.0 CR6CT3CT35111.10527.1840.00.0 CR5CT2CT25111.10527.1840.00.0 CR5CR6CT35119.70585.760.00.0 CT3CT3CT35109.50527.1840.00.0 CT2CT3CT35109.50527.1840.00.0 -- 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] 11-cis retinal topology problem
On 07/06/2013 10:17 PM, Mark Abraham wrote: That's a completely different output. I think both your executables are broken, somehow. Clean the build and install trees and try again :-) Mark Hello Mark: thanks a lot for kind messages. The previous problem was solved by Justin's sugguestions. Here is the errors from debug: Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# NOTE 1 [file topol.top, line 1]: Debugging NOTE 2 [file topol.top, line 2]: Debugging NOTE 3 [file topol.top, line 3]: Debugging .. NOTE 18 [file topol.top, line 18]: DebugginG NOTE 19 [file forcefield.itp, line 1]: Debugging NOTE 20 [file forcefield.itp, line 2]: Debugging NOTE 3474 [file ffbonded.itp, line 820]: Debugging NOTE 3475 [file ffbonded.itp, line 821]: Debugging --- Program grompp, VERSION 4.6.3 Source code file: kernel/topdirs.c, line: 106 Fatal error: Invalid angle type 0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I still don't know where is the problem. thank yo uvery much Albert -- 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] 11-cis retinal topology problem
On 07/07/2013 03:18 AM, Justin Lemkul wrote: This problem can be solved by remembering to complete step 5 of http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field. As Mark notes, though, this issue is entirely separate from your initial problem. -Justin Hello Justin: thanks a lot for kind advices. This problem solved now. However, the grompp still have some problems: grompp_mpi -f em.mdp -c gmx.pdb -o em.tpr source code gromacs-4.6.2/src/kernel/toppush.c, line: 726 Fatal error: Unknown bond_atomtype NCH1 It is pretty strange, I already add NCH1 atom type in ffbonded.itp as following: [ bondtypes ] ; ijfuncb0kb NCH1CT210.149284512.0 NCH1HCR10.1359824.0 NCH1CR1510.132410032.0 In the atomtypes.atp, I also have information: NCH114.00700 ;LYR Why it still complained? thank you very much Albert -- 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] 11-cis retinal topology problem
C12C11C13H12 C13C14C12C20 C14C13C15H14 C15N16C14H15 N16CEC15H16 Then I add this information into the aminoacide.rtp file. I don't know why it failed. It is expected to be treated as regular amino acid residue thank you very much. Albert -- 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] 11-cis retinal topology problem
On 07/06/2013 11:10 AM, Mark Abraham wrote: set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle)); warning_note(wi, "Debugging)"; Mark Hello Mark: thanks a lot for kind messages. I changed above line in topio.c, set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle)); warning_note(wi, "Debugging)"; but the compiling failed with messages: romacs-4.6.3/src/kernel/topio.c: In function ‘read_topol’: gromacs-4.6.3/src/kernel/topio.c:648:35: error: expected ‘)’ before ‘;’ token gromacs-4.6.3/src/kernel/topio.c:1014:9: error: expected ‘;’ before ‘}’ token make[2]: *** [src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o] Error 1 make[2]: *** Waiting for unfinished jobs thank you very much Albert -- 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] 11-cis retinal topology problem
Hello guys: I am building 11-cis-retinal topology these days. Here is what I did: first of all, I build a small peptide like compound which contains:11-cis-retinal connected to the protonated sidechain of LYS, ACE and NME capped the N-term and C-term of the LYS respectively. With this compound, I upload to paramchem and obtained a ligand.str file. Second, I merged the information (including BONDS, ANGLES and DIHEDRALS) of the ligand.str file into related section in par_all36_cgenff.prm. Then I run charmm2gromacs-pvm.py with command: python charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf it generate a folder called cgenff-2b7.ff which includes the following files: aminoacids.rtp ffbonded.itp forcefield.doc atomtypes.atp ffnonbonded.itp forcefield.itp I merged the content of above files into gromacs CHARMM36.ff and build a topology for 11-cis-retinal into aminoacids.rtp as following. This toplogy only contains informations for 11-cis-retinal and protonated LYS: - [ RETK ] [ atoms ] NNH1-0.470 HNH0.311 CACT10.072 HAHB0.093 CBCT2-0.184 HB1HA0.095 HB2HA0.096 CGCT2-0.187 HG1HA0.098 HG2HA0.099 CDCT2-0.1810 HD1HA0.0911 HD2HA0.0912 CECT20.2113 HE1HA0.0514 HE2HA0.0515 NZNH3-0.83216 HZ1HC0.4217 HZ2HC0.4218 CC0.5120 OO-0.5121 C1CG3010.00022 C2CG321-0.18223 C3CG321-0.17724 C4CG321-0.18325 C5CG2DC1-0.00126 C6CG2DC1-0.00127 C7CG2DC2-0.14928 C8CG2DC2-0.15029 C9CG2DC1-0.00330 C10CG2DC1-0.13431 C11CG321-0.19032 C12CG321-0.18733 C13CG2D1-0.00534 C14CG2D1-0.04335 C15CG3240.29936 C16CG331-0.26937 C17CG331 -0.26938 C18CG331 -0.26839 C19CG331 -0.26940 C20CG331 -0.26741 H7HGA40.15042 H8HGA40.15043 H10HGA40.15044 H14HGA40.15045 H21HGA20.09046 H22HGA20.09047 H31HGA20.09048 H32HGA20.09049 H41HGA20.09050 H42HGA20.09051 H111HGA20.09052 H112HGA20.09053 H121HGA20.09054 H122HGA20.09055 H151HGA20.09056 H152HGA20.09057 H161HGA30.09058 H162HGA30.09059 H163HGA30.09060 H171HGA30.09061 H172HGA30.09062 H173HGA30.09063 H181HGA30.09064 H182HGA30.09065 H183HGA30.09066 H191HGA30.09067 H192HGA30.09068 H193HGA30.09069 H201HGA30.09070 H202HGA30.09071 H203HGA30.09072 [ bonds ] CBCA CGCB CDCG CECD NZCE NHN NCA CCA C+N CAHA CBHB1 CBHB2 CGHG1 CGHG2 CDHD1 CDHD2 CEHE1 CEHE2 OC NZHZ1 NZHZ2 NZC15 C1C2 C1C6 C1C16 C1C17 C2C3 C2H21 C2H22 C3C4 C3H31 C3H32 C4C5 C4H41 C4H42 C5C6 C5C18 C6C7 C7C8 C7H7 C8C9 C8H8 C9C10 C9C19 C10C11 C10H10 C11C12 C11H111 C11H112 C12C13 C12H121 C12H122 C13C14 C13C20 C14C15 C14H14 C15H151 C15H152 C16H161 C16H162 C16H163 C17H171 C17H172 C17H173 C18H181 C18H182 C18H183 C19H191 C19H192 C19H193 C20H201 C20H202 C20H203 [ impropers ] N-CCAHN CCA+NO [ cmap ] -CNCAC+N - with the new forcefild, I run pdb2gmx: - pdb2gmx -f input.pdb -o gmx.pdb - it finished without any warnings or errors for this step. However, when I try to run grompp with command: - grompp_mpi -f em.mdp -c gmx.pdb -p topol.top - it failed with messages: - Program grompp_mpi, VERSION 4.6.2 Source code file: /home/albert/Desktop/gromacs-4.6.2/src/kernel/topdirs.c, line: 106 Fatal error: Invalid angle type 0 For
[gmx-users] charmm2gromacs-pvm.py error
Hlello: I am trying to run charmm2gromacs-pvm.py with command: charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf but it failed with messages: Creating cgenff-2b7.ff files... Traceback (most recent call last): File "charmm2gromacs-pvm.py", line 283, in name = segments[1] IndexError: list index out of range although it generate a cgenff-2b7 folder, but all the files it generate are empty. thank you very much Albert -- 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] GPU cannot be detected
Hello: I've installed Gromacs-4.6.2 in GPU cluster with following configurations: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0 -DFFTWF_LIBRARY=/home/albert/install/fftw-3.3.3/lib/libfftw3f.so However, when I submit job with qsub, Gromacs failed with following messages: No GPUs detected on host c0204 Can not set thread affinities on the current platform. On NUMA systems this can cause performance degradation. If you think your platform should support setting affinities, contact the GROMACS developers. -- mpirun noticed that process rank 2 with PID 6 on node c0205 exited on signal 4 (Illegal instruction). -- I am just wondering how can we solve this problem? thank you very much Albert -- 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] fftw compile error for 4.6.2
On 07/04/2013 07:59 PM, Mark Abraham wrote: I plan to release 4.6.3 tomorrow, once I've gotten some more urgent stuff off my plate:-). Mark thanks a lot for kind messages, Mark. It seems that Gromacs update more and more frequently.... Albert -- 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] a question concerning on entropy
Hello : I've got a question about the the entropy. As we all know that in the md.edr file it will give us the entropy value of the system along the simulations. However, my system is a protein/membrane system, and I am only would like to make statics for the protein/water related entropy. I am just wondering, is it possible to do this? thank you very much Albert -- 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] fftw compile error for 4.6.2
On 07/04/2013 05:52 PM, Szilárd Páll wrote: FYI: 4.6.2 contains a bug related to thread affinity setting which will lead to a considerable performance loss (I;ve seen 35%) as well as often inconsistent performance - especially with GPUs (case in which one would run many OpenMP threads/rank). My advice is that you either use the code from git or wait for 4.6.3. Oh, my Lady GaGa... Do you have any idea when this new version would be released? THX Albert -- 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] another error compiling 4.6.2 in GPU cluster
Hello:
I am using the following configuration to compile gromacs-4.6.2 in a
GPU cluster:
CC=icc FC=ifort F77=ifort CXX=icpc
CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6
cmake .. -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON
-DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0/cuda
-DFFTWF_LIBRARY=/home/albert/install/fftw-3.3.3/lib/libfftw3f.so
It was finished without any errors, But when I type
make -j4
it stopped at 66%:
clared but never referenced
static const double* sy_const[] = {
/home/albert/install/source/gromacs-4.6.2/include/maths.h(189): remark
#177: function "gmx_numzero" was declared but never referenced
gmx_numzero(double a)
^
/home/albert/install/source/gromacs-4.6.2/include/maths.h(196): remark
#177: function "gmx_log2" was declared but never referenced
gmx_log2(real x)
^
/home/albert/install/source/gromacs-4.6.2/include/vec.h(849): remark
#177: function "calc_lll" was declared but never referenced
static void calc_lll(rvec box, rvec lll)
^
/home/albert/install/source/gromacs-4.6.2/include/vec.h(880): remark
#177: function "m_rveccopy" was declared but never referenced
static void m_rveccopy(int dim, rvec *a, rvec *b)
^
/home/albert/install/source/gromacs-4.6.2/include/vec.h(892): remark
#177: function "matrix_convert" was declared but never referenced
static void matrix_convert(matrix box, rvec vec, rvec angle)
^
/home/albert/install/source/gromacs-4.6.2/include/grompp.h(155): remark
#177: variable "ds" was declared but never referenced
static const char *ds[d_maxdir+1] = {
Linking CXX static library libmd_mpi.a
[ 66%] Built target md
make: *** [all] Error 2
thank you very much
Albert
--
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Re: [gmx-users] fftw compile error for 4.6.2
On 07/04/2013 11:18 AM, Mark Abraham wrote: No idea. I do not think there is any need for you to use BUILD_SHARED_LIBS=OFF, and it could well be the problem. Mark thank you all the same. I found the problem, there is a subdirectory in cuda5.0: /export/cuda5.0/cuda the problem solved after I redirect the path into above path. best Albert -- 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] fftw compile error for 4.6.2
On 07/04/2013 10:43 AM, Oliver Schillinger wrote: It seems that GROMACS is looking for a shared library, but you compiled FFTW statically (--enable-static). Either recompile FFTW --enable-shared or link GROMACS statically by passing -DBUILD_SHARED_LIBS=OFF to cmake. Hello guys: thanks a lot for such warning advices. the fftw error passed after I take above suggestions, but there is something wrong with CUDA. It is very strange to me, because I've already specified the cuda path. CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0 -DFFTWF_LIBRARY=/home/albert/install/fftw-3.3.3/lib/libfftw3f.so -DBUILD_SHARED_LIBS=OFF CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: CUDA_CUDART_LIBRARY (ADVANCED) linked by target "cuda_tools" in directory /home/albert/install/source/gromacs-4.6.2/src/gmxlib/cuda_tools linked by target "gpu_utils" in directory /home/albert/install/source/gromacs-4.6.2/src/gmxlib/gpu_utils linked by target "nbnxn_cuda" in directory /home/albert/install/source/gromacs-4.6.2/src/mdlib/nbnxn_cuda CUDA_TOOLKIT_INCLUDE (ADVANCED) used as include directory in directory /home/albert/install/source/gromacs-4.6.2/src/gmxlib/cuda_tools used as include directory in directory /home/albert/install/source/gromacs-4.6.2/src/gmxlib/gpu_utils used as include directory in directory /home/albert/install/source/gromacs-4.6.2/src/gmxlib/gpu_utils used as include directory in directory /home/albert/install/source/gromacs-4.6.2/src/mdlib/nbnxn_cuda -- 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] fftw compile error for 4.6.2
Hello: I am trying to compile Gromacs-4.6.2 for a GPU cluster with following command: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0 -DFFTWF_LIBRARY= /export/fftw-3.3.3 but it always claimed errors for fftw: -- Found PkgConfig: /usr/bin/pkg-config (found version "0.21") -- checking for module 'fftw3f' -- package 'fftw3f' not found -- pkg-config could not detect fftw3f, trying generic detection -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib WARNING: Target "cmTryCompileExec1612346837" requests linking to directory "/export/fftw-3.3.3/lib". Targets may link only to libraries. CMake is dropping the item. -- Looking for fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib - not found CMake Error at cmake/FindFFTW.cmake:97 (message): Could not find fftwf_plan_r2r_1d in /export/fftw-3.3.3/lib, take a look at the error message in /home/albert/install/gromacs-4.6.2/build/CMakeFiles/CMakeError.log to find out what went wrong. If you are using a static lib (.a) make sure you have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') ! Call Stack (most recent call first): CMakeLists.txt:943 (find_package) -- Configuring incomplete, errors occurred! I compiled fftw with options: ./configure CC=icc CXX=icpc F77=ifort FC=ifort --prefix=/home/albert/install/fftw-3.3.3 --enable-float --with-pic --enable-single --enable-static --enable-mpi and I don't find so called "libfftw3f.so" in the fftw installation directory. does anybody have any advices? THX Albert -- 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] multiple chain restrain problem
On 06/27/2013 01:50 PM, Justin Lemkul wrote: Then select by residue number. Note that genrestr will only work for the first molecule, since position restraint numbering is based on the [moleculetype] numbering, not the coordinate file numbering. -Justin thank you very much for kind advices. I solved this by extracting each chain into indivisual coordinate and make restrain based on them. best Albert -- 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] multiple chain restrain problem
Hello: I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, and gromacs generate toplogy and restrain file for each chain: gmx.pdb topol_chain_A.itp topol_chain_B.itp porschain_A.itp porschain_B.itp I noticed that the gmx.pdb doesn't contain any chain information. I am going to equilibrate the system first restrain the heavy atoms which can be specified by porschain_A.itp and porschain_B.itp. However, in the next step I am going to restrain only the backbone of chain A, how can we to do this? The chain information in new generated gmx.pdb lost When I use command: genrestr -f gmx.pdb -p porsB it doesn't contains selection for chain thank you very much Albert -- 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] problem with charmm2gromacs-pvm.py
Hello: I am trying to use charmm2gromacs-pvm.py to generate cgenff with comman: python charmm2gromacs-pvm.py toppar/par_all36_cgenff.prm toppar/top_all36_cgenff.rtf but it always failed with messages: Creating cgenff-2b7.ff files... Traceback (most recent call last): File "charmm2gromacs-pvm.py", line 283, in name = segments[1] IndexError: list index out of range thank you very much Albert -- 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] shall we use double precision?
HI Mark: thank you for kind reply. I found the following in the documentations: Installations: Example. This is the procedure for compiling the serial version of GROMACS, using the GNU compilers. tar zxf gromacs-4.0.5.tar.gz cd gromacs-4.0.5 export plumedir="PLUMED root" cp $plumedir/patches/plumedpatch gromacs 4.0.4.sh . CC=gcc CXX=g++ ./configure ./plumedpatch gromacs 4.0.4.sh -patch make make install However, in the test section, it said the following: For GROMACS users only. Please note that: The tests for GROMACS are designed for and should be executed with the double-precision version of the code; Biasxmd, ptmetad, dd and pd are designed for the parallel version of GROMACS. The user should specify in the test script the location of the parallel executable and the version of GROMACS used. These tests will fail if the parallel version of GROMACS has not been compiled. thank you very much Albert On 06/11/2013 08:55 AM, Mark Abraham wrote: Probably not. What does PLUMED documentation recommend? Mark -- 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] shall we use double precision?
Hello : I am going to use Gromacs with PLUMD plugin to perform Metadynamics. Since this methods involved in free energy calculations, I am just wondering is it necessary to introduce double precision Gromacs? thank you very much Albert -- 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] GPU ECC question
Hello: Recently I found a strange question about Gromacs-4.6.2 on GPU workstaion. In my GTX690 machine, when I run md production I found that the ECC is on. However, in my another GTX590 machine, I found the ECC was off: 4 GPUs detected: #0: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC: no, stat: compatible moreover, there is only two GTX590 in the machine, I don't know why Gromacs claimed 4 GPU detected. However, in my another Linux machine which also have two GTX590, Gromacs-4.6.2 only find 2 GPU, and ECC is still off. I am just wondering: (1) why in GTX690 the ECC can be on while it is off in my GTX590? I compiled Gromacs with the same options and the same version of intel compiler (2) why in machines both of physically installed two GTX590 cards, one of them was detected with 4 GPU while the other was claimed contains two GPU? thank you very much best Albert -- 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] why mass and charge is zero?
On 06/08/2013 06:56 PM, David van der Spoel wrote: the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. IC. thank you very much. Albert -- 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] why mass and charge is zero?
Hello: I generate a ligand toplogy by ACPYPE with amber GAFF. However, I found that in the ligandGMX.itp file, in the atomtypes section, the mass and charge are all zero, like: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb NT NT 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 however, in the atoms sections, I found: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 26 NT 1 UKA N10 26-0.719301 14.01000 ; qtot -7.758 I am a little bit confused for this. Does anybody have any idea for it? thank you very much best Albert -- 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] GPU problem
On 06/04/2013 11:22 AM, Chandan Choudhury wrote: Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan thank you so much. it works well now. ALBERT -- 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] GPU problem
Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- 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] GROMACS 4.6.2 released
it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to upgrade their installations from 4.6 and 4.6.1. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.2.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.2.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.2.x http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.2.tar.gz Happy simulating! The GROMACS development team -- 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] how to distribute CPU in GPU workstation?
Dear: I've got 4 GPU in one GPU workstation. I've submit one of my job by command: mdrun -s md.tpr -gpu_id 01 -n -x md.xtc I found that all the 24 CPU were occupied by this job. However, I would like to submit another job with -gpu_id 23, how should I specify the CPU for each job? thank you very much best Albert -- 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_select question
Dear: I am trying to run g_select with command: g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat in the selection.dat I defined the following: watero= name 0 and resname T3P; close = water0 and within 0.6 of resid 50; close; my residue 50 is in the deep pocket of protein and there is only max. 12 water near 6A. However, I found that in almost all my trajectories, there are at least 16 water from the g_select output. I am just wondering, is there anything wrong of my defenition in selection.dat? thank you very much best Albert -- 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] GPU job often stopped
the problem is still there... :-( On 04/29/2013 06:06 PM, Szilárd Páll wrote: On Mon, Apr 29, 2013 at 3:51 PM, Albert wrote: >On 04/29/2013 03:47 PM, Szilárd Páll wrote: >> >>In that case, while it isn't very likely, the issue could be caused by >>some implementation detail which aims to avoid performance loss caused >>by an issue in the NVIDIA drivers. >> >>Try running with the GMX_CUDA_STREAMSYNC environment variable set. >> >>Btw, were there any other processes using the GPU while mdrun was running? >> >>Cheers, >>-- >>Szilárd > > >thanks for kind reply. >There is no any other process when I am running Gromacs. > >do you mean I should set GMX_CUDA_STREAMSYNC in the job script like: > >export GMX_CUDA_STREAMSYNC=/opt/cuda-5.0 Sort of, but the value does not matter. So if your shell is bash, the above as well as simply "export GMX_CUDA_STREAMSYNC=" will work fine. Let us know if this avoided the crash - when you have simulated long enough to be able to judge. Cheers, -- Szilárd -- 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] where can be obtain circled lipids bilayer?
Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- 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] GPU job often stopped
On 04/29/2013 03:47 PM, Szilárd Páll wrote: In that case, while it isn't very likely, the issue could be caused by some implementation detail which aims to avoid performance loss caused by an issue in the NVIDIA drivers. Try running with the GMX_CUDA_STREAMSYNC environment variable set. Btw, were there any other processes using the GPU while mdrun was running? Cheers, -- Szilárd thanks for kind reply. There is no any other process when I am running Gromacs. do you mean I should set GMX_CUDA_STREAMSYNC in the job script like: export GMX_CUDA_STREAMSYNC=/opt/cuda-5.0 ? THX Albert -- 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] GPU job often stopped
On 04/29/2013 03:31 PM, Szilárd Páll wrote: The segv indicates that mdrun crashed and not that the machine was restarted. The GPU detection output (both on stderr and log) should show whether ECC is "on" (and so does the nvidia-smi tool). Cheers, -- Szilárd yes it was on: Reading file heavy.tpr, VERSION 4.6.1 (single precision) Using 4 MPI threads Using 8 OpenMP threads per tMPI thread 5 GPUs detected: #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #1: NVIDIA GeForce GTX 650, compute cap.: 3.0, ECC: no, stat: compatible #2: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #3: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible #4: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible 4 GPUs user-selected for this run: #0, #2, #3, #4 -- 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] GPU job often stopped
On 04/28/2013 05:45 PM, Justin Lemkul wrote: Frequent failures suggest instability in the simulated system. Check your .log file or stderr for informative Gromacs diagnostic information. -Justin my log file didn't have any errors, the end of topped log file something like: DD step 2259 vol min/aver 0.967 load imb.: force 0.8% Step Time Lambda 226045200.00.0 Energies (kJ/mol) AngleU-BProper Dih. Improper Dih. LJ-14 9.86437e+034.02406e+043.52809e+046.13542e+02 8.61815e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1.25055e+043.05477e+04 -9.05956e+03 -6.02400e+05 1.58357e+03 Position Rest. PotentialKinetic En. Total Energy Temperature 1.39149e+02 -4.72066e+051.37165e+05 -3.34901e+05 3.11958e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.94092e+02 -7.91535e+011.79812e-05 also in the information file I only obtained information: step 13300, will finish Tue Apr 30 14:41 NOTE: Turning on dynamic load balancing Probably the machine was restarted from time to time? best Albert -- 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] GPU job often stopped
Hello: yes, I tried the CPU only version, it goes well and didn't stop. I am not sure whether I have ECC on or not. There are 4 Tesla K20 and one GTX650 in the workstation, after compilation, I simple submit the jobs with command: mdrun -s md.tpr -gpu_id 0234 I submit the same system in another GTX690 machine, it also goes well. I compiled Gromacs with the same options in that machine. thank you very much best Albert On 04/29/2013 01:19 PM, Szilárd Páll wrote: Have you tried running on CPUs only just to see if the issue persists? Unless the issue does not occur with the same binary on the same hardware running on CPUs only, I doubt it's a problem in the code. Do you have ECC on? -- Szilárd -- 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] GPU job often stopped
Dear: I am running MD jobs in a workstation with 4 K20 GPU and I found that the job always failed with following messages from time to time: [tesla:03432] *** Process received signal *** [tesla:03432] Signal: Segmentation fault (11) [tesla:03432] Signal code: Address not mapped (1) [tesla:03432] Failing at address: 0xfffe02de67e0 [tesla:03432] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f4666da1cb0] [tesla:03432] [ 1] mdrun_mpi() [0x47dd61] [tesla:03432] [ 2] mdrun_mpi() [0x47d8ae] [tesla:03432] [ 3] /opt/intel/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x7f46667904f3] [tesla:03432] *** End of error message *** -- mpirun noticed that process rank 0 with PID 3432 on node tesla exited on signal 11 (Segmentation fault). -- I can continue the jobs with mdrun option "-append -cpi", but it still stopped from time to time. I am just wondering what's the problem? thank you very much Albert -- 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] why files are so large?
On 04/28/2013 02:08 PM, Justin Lemkul wrote: This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -Justin hi Justin: thanks a lot for kind comments. I am using the latest 4.6.1 with GPU production. best Albert -- 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] why files are so large?
Hello: I am using the following settings for output file: dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout = 500 ; Write coordinates to output .trr file every 2 ps nstvout = 500 ; Write velocities to output .trr file every 2 ps nstfout = 0 nstxtcout = 5 nstenergy = 50; Write energies to output .edr file every 2 ps nstlog = 50; Write output to .log file every 2 ps and I obtained following warnings from grompp: NOTE 2 [file md.mdp]: This run will generate roughly 2791985478365075968 Mb of data however, when I set nstxout=0 nstvout=0 nstoout=0 I obtained following informations: This run will generate roughly -9066 Mb of data why it file size is negative? Moreover, my nstxout is very large, I don't know why the file is so big and no matter how did I change nstxout, nstvout, the files size doesn't change at all. it always claimed: This run will generate roughly 2791985478365075968 Mb of data thank you very much Albert -- 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] can we use large timestep for membrane GPU simulation?
Hello: I am watching Eric online Gromacs GPU webminar these days. I notice that he talked about introduce large timestep (5fs) for GPU simulations on a water system. I am just wondering, can we also introduce such big time step for membrane system if we are going to run the job in Gromacs? What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the timestep and cutoff. could anybody comment on this? thank you very much best Albert -- 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] _gpu_id failed
Hello: I am going to run gromacs with command: mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4 but it failed with messages: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364 Fatal error: Expected a string argument for option -gpu_id For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Jede der Scherben spiegelt das Licht" (Wir sind Helden) Error on node 3, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 3 out of 4 gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden) gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden) gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden) -- mpirun has exited due to process rank 2 with PID 10440 on node tesla exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). thank you very much Albert -- 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] GPU efficiency question
Dear: I've got two GTX690 in a a workstation and I found that when I run the md production with following two command: mpirun -np 4 md_run_mpi or mpirun -np 2 md_run_mpi the efficiency are the same. I notice that gromacs can detect 4 GPU (probably because GTX690 have two core..): 4 GPUs detected on host node4: #0: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 690, compute cap.: 3.0, ECC: no, stat: compatible why the "-np 2" and "-np 4" are the same efficiency? shouldn't it be faster for "-np 4" ? thank you very much Albert -- 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] compile error
IC. it works very well now. thanks a lot Albert On 04/26/2013 08:01 PM, Szilárd Páll wrote: You got a warning at configure-time that the nvcc host compiler can't be set because the mpi compiler wrapper are used. Because of this, nvcc is using gcc to compile CPU code whick chokes on the icc flags. You can: - set CUDA_HOST_COMPILER to the mpicc backend, i.e. icc or - let cmake detect MPI and use simply CC=icc CXX=icpc cmake -DGMX_MPI=ON (in this case the normal compiler are used and*if* cmake can detect the MPI libs it will not need the wrappers). Cheers, -- Szilárd -- 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] compile error
Dear: I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is my step: ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc F77=ifort FC=ifort make make install cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-5.0 -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs-4.6.1 -DCMAKE_PREFIX_PATH=/opt/intel/mkl/include/fftw -DCMAKE_CXX_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpiCC -DCMAKE_C_COMPILER=/home/albert/install/openmpi-1.4.5/bin/mpicc however, it failed with messages: [ 1%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o cc1plus: error: unrecognized command line option ‘-ip’ CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message): Error generating /home/albert/install/source/gromacs-4.6.1/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make: *** [all] Error 2 when I try to run make thank you very much best Albert -- 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] using CHARMM force field for organic molecule
On 04/22/2013 01:43 PM, Justin Lemkul wrote: There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin did paramchem support gromacs? As far as I know it only export in CHARMM format. Albert -- 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] GROMACS 4.6 with GPU acceleration (double
On 04/22/2013 08:40 AM, Mikhail Stukan wrote: Could you explain which hardware do you mean? As far as I know, K20X supports double precision, so I would assume that double precision GROMACS should be realizable on it. Really? But many people have discussed that the GPU version ONLY support single precision.. Thanks and regards, Mikhail -- 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] how to direct log file correctly?
Hi Justin: thanks for reply. I redirect it by command: mpirun -np 2 mdrun_mpi -v -s md.tpr -c md.gro -x md.xtc -g md.log > md.info However the information is still in my terminal screen instead of md.info file. It generate a md.info file, but it it is empty. I also try to use command: mpirun -np 2 mdrun_mpi -v -s md.tpr -c md.gro -x md.xtc -g md.log & > md.info but it said: Invalid null command. thanks a lot Albert On 04/17/2013 05:33 PM, Justin Lemkul wrote: On 4/17/13 11:30 AM, Albert wrote: Hello: I found that each time I submit gromacs job in GPU workstation, the log file always in my terminal screen, like: imb F 1% step 13700, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 13800, will finish Wed Apr 17 17:57:20 2013 imb F 0% step 13900, will finish Wed Apr 17 17:57:20 2013 imb F 0% step 14000, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 14100, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14200, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14300, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14400, will finish Wed Apr 17 17:57:19 2013 I am using command: mpirun -np 2 mdrun_mpi -v -s nvt.tpr -c nvt.gro -g nvt.log -x nvt.xtc grompp_mpi -f npt1.mdp -c nvt.gro -p topol.top -o heavy.tpr -n mpirun -np 2 mdrun_mpi -v -s heavy.tpr -c heavy.gro -x heavy.xtc -g 1000.log I am just wondering how can we direct the log file correctly? Meanwhile tho job won't have any problem going to next step (I am running all the steps in one script). You're only getting that output because you're enabling verbose mode with -v. If you don't want that information, don't use -v. If you do want it, but just want it written to a file, redirect it using standard command line redirection (Google is your friend). -Justin -- 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] Announcement: new version of GridMAT-MD available
It seems to be good. However, I always have problem to compile matpack which is needed by xmatrix... I sent the author an email, but never replied.. here is the log file: creating libpng12.la (cd .libs && rm -f libpng12.la && ln -s ../libpng12.la libpng12.la) make[4]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' make[3]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' (cd Matutil ; make ) make[3]: Entering directory `/home/albert/Desktop/matpack/source/Matutil' g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE="" -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpromannumber.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE="" -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpcontextsave.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE="" -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpparsetool.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE="" -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpgetopt.cpp mpgetopt.cpp: In member function ‘bool MATPACK::MpGetopt::assign(MATPACK::MpGetopt::OptNode*, const char**, std::string&)’: mpgetopt.cpp:314: error: ‘strtol’ was not declared in this scope mpgetopt.cpp:330: error: ‘strtoul’ was not declared in this scope mpgetopt.cpp:345: error: ‘strtod’ was not declared in this scope g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE="" -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mptimerqueue.cpp make[3]: *** [mpgetopt.o] Error 1 make[3]: *** Waiting for unfinished jobs make[3]: Leaving directory `/home/albert/Desktop/matpack/source/Matutil' make[2]: *** [static_lib] Error 2 make[2]: Leaving directory `/home/albert/Desktop/matpack/source' make[1]: *** [lib] Error 2 make[1]: Leaving directory `/home/albert/Desktop/matpack' make: *** [allstatic] Error 2 thank you very much Albert On 04/18/2013 11:19 PM, Justin Lemkul wrote: Greetings all, I wanted to announce that we have released version 2.0 of GridMAT-MD. Many of you use this program for membrane analysis and I am pleased to note that we have introduced many new features based on your feedback, including trajectory support (multi-frame .pdb and .gro files). Please visit our webpage for details: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ We hope you continue to find our software useful. Please contact me if any issues arise. -Justin -- 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] how to direct log file correctly?
Hello: I found that each time I submit gromacs job in GPU workstation, the log file always in my terminal screen, like: imb F 1% step 13700, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 13800, will finish Wed Apr 17 17:57:20 2013 imb F 0% step 13900, will finish Wed Apr 17 17:57:20 2013 imb F 0% step 14000, will finish Wed Apr 17 17:57:20 2013 imb F 1% step 14100, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14200, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14300, will finish Wed Apr 17 17:57:19 2013 imb F 0% step 14400, will finish Wed Apr 17 17:57:19 2013 I am using command: mpirun -np 2 mdrun_mpi -v -s nvt.tpr -c nvt.gro -g nvt.log -x nvt.xtc grompp_mpi -f npt1.mdp -c nvt.gro -p topol.top -o heavy.tpr -n mpirun -np 2 mdrun_mpi -v -s heavy.tpr -c heavy.gro -x heavy.xtc -g 1000.log I am just wondering how can we direct the log file correctly? Meanwhile tho job won't have any problem going to next step (I am running all the steps in one script). thank you very much best Albert -- 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] Re: why minimization stop so fast
Hello Brad: thanks for advices. I've also solved the problem after I run the 6.1 minimization step in NAMD. After that, I reimport the lipids system into gromacs, and it no longer complain those issue. best Albert On 04/16/2013 09:59 PM, Brad Van Oosten wrote: Hello,I have had the same problem with CHARMM-GUI however I have found a decent work-around procedure: 1. Go to your input .gro file and locate the atom with infinite force (atom 23533 in this case)2. Change one of the x,y,z positions of that atom by about /- 0.5.3. Rerun grompp with the new .gro file5. rerun minimization4. Repeat. this may happen with several atoms that are overlapped, but with the little shove you give it, it may be able to correct itself -- 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] new CHARMM-GUI output not supported?
Hello Mark and Justin: thanks a lot for kind comments. I changed the atom order in forcecfiled .rtp file so that they are the same with the output from CHARMM-GUI, and it works fine now. best Albert On 04/17/2013 12:50 AM, Mark Abraham wrote: "Support" is not really the right word:-). That force field port and that builder are things provided by (different?) third parties in the hope that they are useful. You can't really expect stuff written by three groups of people at different times to inter-operate seamlessly. IIRC nbfix has been around for a while, but I've no idea what it is... Mark -- 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] why minimization stop so fast
On 04/16/2013 07:28 PM, Justin Lemkul wrote: Create a more physically reasonable starting structure. -Justin the protein and ligand are already minimized, but CHARMM-GUI create the mix lipids automatically which I cannot change them. ALBERT -- 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] why minimization stop so fast
Hi Justin: thanks for kind reply. Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force on protein and ligands, and try to minimize the rest of the system do you have any idea how can I solve the issue and make it work? thanks a lot Albert On 04/16/2013 07:09 PM, Justin Lemkul wrote: Your system has severe atomic overlap. You have infinite force on atom 23533. -Justin -- 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] why minimization stop so fast
Hello: I've built a system with CHARMM-GUI, and I am trying to mimize it with following em.mdp file title = steepest descent energy minimization define = -DPOSRES -DPOSRES_LIG cpp = /usr/bin/cpp include = integrator = steep nsteps = 5 emtol = 0.01 nstcgsteep = 1000;step for cg correction ,the larger the more accurate nstxout = nstvout = nstlog = 100 nstenergy = 10 nstxtcout = 100 nstlist = 10 ns_type = grid rcoulomb= 1.4 coulombtype = pme fourierspacing= 0.12 pme_order= 4 rvdw= 1.4 rlist = 1.4 DispCorr= enerpres constraints = none; none,hbonds,all-bonds,h-angles,all-angles cutoff-scheme =Verlet ; GPU running constraint_algorithm = Lincs but it stopped after 15 steps. Steepest Descents: Tolerance (Fmax) = 1.0e-02 Number of steps=5 Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 0.01 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 0.01. Potential Energy = 3.4943549e+18 Maximum force =inf on atom 23533 Norm of force =inf NOTE: 22 % of the run time was spent in domain decomposition, 6 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#154: "Rub It Right Accross Your Eyes" (F. Zappa) Thank you very much Albert -- 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] new CHARMM-GUI output not supported?
Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB And here is initial 12 line Slipid popc.itp: ; residue 1 POPC rtp POPC q 0.0 1NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6 2 CTL2 1 POPCC12 2 -0.1 12.011 ; qtot -0.7 3 CTL5 1 POPCC13 3 -0.35 12.011 ; qtot -1.05 4 CTL5 1 POPCC14 4 -0.35 12.011 ; qtot -1.4 5 CTL5 1 POPCC15 5 -0.35 12.011 ; qtot -1.75 6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75 10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5 11 HL 1 POPC H14A 11 0.25 1.008 ; qtot -0.25 12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0 And here is initial 12 line in CHARMM36.ff/lipids.rtp file: [ POPC ] [ atoms ] NNTL-0.600 C12CTL2-0.101 C13CTL5-0.352 C14CTL5-0.353 C15CTL5-0.354 H12AHL0.255 H12BHL0.256 H13AHL0.257 H13BHL0.258 H13CHL0.259 H14AHL0.2510 H14BHL0.2511 As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp , but both of which are different from current CHARMM-GUI output. Probably CHARMM-GUI change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot support current new version CHARMM-GUI output? Moreover, the new CHARMM36 FF (both for protein, lipids and ions)introduced Residue pair specific (native contact) non-bonded parameters, nbfix term, probably it is also not supported in current CHARMM36FF in Gromacs? thank you very much best Albert -- 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] new CHARMM-GUI output not supported?
Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB And here is initial 12 line Slipid popc.itp: ; residue 1 POPC rtp POPC q 0.0 1NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6 2 CTL2 1 POPCC12 2 -0.1 12.011 ; qtot -0.7 3 CTL5 1 POPCC13 3 -0.35 12.011 ; qtot -1.05 4 CTL5 1 POPCC14 4 -0.35 12.011 ; qtot -1.4 5 CTL5 1 POPCC15 5 -0.35 12.011 ; qtot -1.75 6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75 10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5 11 HL 1 POPC H14A 11 0.25 1.008 ; qtot -0.25 12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0 And here is initial 12 line in CHARMM36.ff/lipids.rtp file: [ POPC ] [ atoms ] NNTL-0.600 C12CTL2-0.101 C13CTL5-0.352 C14CTL5-0.353 C15CTL5-0.354 H12AHL0.255 H12BHL0.256 H13AHL0.257 H13BHL0.258 H13CHL0.259 H14AHL0.2510 H14BHL0.2511 As we can see the Slipids popc.itp is the same with CHARMM36.ff/lipids.rtp , but both of which are different from current CHARMM-GUI output. Probably CHARMM-GUI change its format, and Slipids FF and CHARMM36 FF in Gromacs cannot support current new version CHARMM-GUI output? Moreover, the new CHARMM36 FF (both for protein, lipids and ions)introduced Residue pair specific (native contact) non-bonded parameters, nbfix term, probably it is also not supported in current CHARMM36FF in Gromacs? thank you very much best Albert --- Begin Message --- Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414 18.821 1.00-17.85 MEMB ATOM 6317 H12A POPC 22 4.337 -21.455 18.379 1.00 0.00 MEMB ATOM 6318 H12B POPC 22 5.583 -22.427 19.173 1.00 0.00 MEMB ATOM 6319 C13 POPC 22 3.979 -23.730 20.844 1.00-17.96 MEMB ATOM 6320 H13A POPC 22 3.969 -24.679 20.329 1.00 0.00 MEMB ATOM 6321 H13B POPC 22 4.977 -23.582 21.229 1.00 0.00 MEMB ATOM 6322 H13C POPC 22 3.420 -23.829 21.763 1.00 0.00 MEMB ATOM 6323 C14 POPC 22 3.424 -21.320 20.778 1.00-20.44 MEMB ATOM 6324 H14A POPC 22 2.552 -21.497 21.391 1.00 0.00 MEMB ATOM 6325 H14B POPC 22 4.281 -21.118 21.404 1.00 0.00 MEMB ATOM 6326 H14C POPC 22 3.249 -20.474 20.130 1.00 0.00 MEMB And here is initial 12 line Slipid popc.itp: ; residue 1 POPC rtp POPC q 0.0 1NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6 2 CTL2 1 POPCC12 2 -0.1 12.011 ; qtot -0.7 3 CTL5 1 POPCC13 3 -0.35 12.011 ; qtot -1.05 4 CTL5 1 POPCC14 4 -0.35 12.011 ; qtot -1.4 5 CTL5 1 POPCC15 5 -0.35 12.011 ; qtot -1.75 6 HL 1 POPC H12A 6 0.25 1.008 ; qtot -1.5 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75 10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5 11 HL 1 POPC H14A 11
Re: [gmx-users] why no. of atoms doesn't match?
-5.982 15.011 -0.495 1.00 0.00 MEMB ATOM 6371 H15S POPA 22 -7.788 14.771 -0.220 1.00 0.00 MEMB ATOM 6372 C216 POPA 22 -6.719 13.003 -0.168 1.00 1.38 MEMB ATOM 6373 H16R POPA 22 -7.194 12.488 0.703 1.00 0.00 MEMB ATOM 6374 H16S POPA 22 -5.668 12.647 -0.108 1.00 0.00 MEMB ATOM 6375 C217 POPA 22 -7.629 12.493 -1.353 1.00 2.26 MEMB ATOM 6376 H17R POPA 22 -7.103 12.927 -2.231 1.00 0.00 MEMB ATOM 6377 H17S POPA 22 -8.714 12.714 -1.259 1.00 0.00 MEMB ATOM 6378 C218 POPA 22 -7.509 11.008 -1.453 1.00 3.09 MEMB ATOM 6379 H18R POPA 22 -7.847 10.511 -0.519 1.00 0.00 MEMB ATOM 6380 H18S POPA 22 -6.520 10.572 -1.713 1.00 0.00 MEMB ATOM 6381 H18T POPA 22 -8.258 10.612 -2.171 1.00 0.00 MEMB ATOM 6382 C33 POPA 22 -16.464 17.039 11.820 1.00-12.04 MEMB ATOM 6383 H3X POPA 22 -17.560 16.953 11.693 1.00 0.00 MEMB ATOM 6384 H3Y POPA 22 -16.019 16.368 11.052 1.00 0.00 MEMB ATOM 6385 C34 POPA 22 -16.090 18.484 11.481 1.00-10.72 MEMB ATOM 6386 H4X POPA 22 -15.125 18.749 11.972 1.00 0.00 MEMB ATOM 6387 H4Y POPA 22 -16.873 19.152 11.903 1.00 0.00 MEMB ATOM 6388 C35 POPA 22 -15.928 18.728 9.974 1.00 -9.86 MEMB ATOM 6389 H5X POPA 22 -14.961 18.301 9.648 1.00 0.00 MEMB ATOM 6390 H5Y POPA 22 -15.835 19.806 9.775 1.00 0.00 MEMB ATOM 6391 C36 POPA 22 -17.057 18.200 9.080 1.00 -8.54 MEMB ATOM 6392 H6X POPA 22 -18.041 18.549 9.465 1.00 0.00 MEMB ATOM 6393 H6Y POPA 22 -17.055 17.088 9.085 1.00 0.00 MEMB ATOM 6394 C37 POPA 22 -16.865 18.708 7.645 1.00 -7.43 MEMB ATOM 6395 H7X POPA 22 -15.803 18.583 7.354 1.00 0.00 MEMB ATOM 6396 H7Y POPA 22 -17.018 19.795 7.633 1.00 0.00 MEMB ATOM 6397 C38 POPA 22 -17.785 18.057 6.608 1.00 -6.21 MEMB ATOM 6398 H8X POPA 22 -18.835 18.366 6.809 1.00 0.00 MEMB ATOM 6399 H8Y POPA 22 -17.730 16.950 6.711 1.00 0.00 MEMB ATOM 6400 C39 POPA 22 -17.404 18.434 5.167 1.00 -5.05 MEMB ATOM 6401 H9X POPA 22 -16.388 18.042 4.949 1.00 0.00 MEMB ATOM 6402 H9Y POPA 22 -17.367 19.541 5.069 1.00 0.00 MEMB ATOM 6403 C310 POPA 22 -18.395 17.870 4.142 1.00 -3.85 MEMB ATOM 6404 H10X POPA 22 -19.360 18.409 4.265 1.00 0.00 MEMB ATOM 6405 H10Y POPA 22 -18.570 16.797 4.381 1.00 0.00 MEMB ATOM 6406 C311 POPA 22 -17.940 17.953 2.674 1.00 -2.66 MEMB ATOM 6407 H11X POPA 22 -18.798 17.664 2.025 1.00 0.00 MEMB ATOM 6408 H11Y POPA 22 -17.133 17.205 2.507 1.00 0.00 MEMB ATOM 6409 C312 POPA 22 -17.419 19.330 2.231 1.00 -1.30 MEMB ATOM 6410 H12X POPA 22 -16.444 19.506 2.741 1.00 0.00 MEMB ATOM 6411 H12Y POPA 22 -18.108 20.133 2.554 1.00 0.00 MEMB ATOM 6412 C313 POPA 22 -17.202 19.416 0.713 1.00 -0.21 MEMB ATOM 6413 H13X POPA 22 -16.950 18.396 0.342 1.00 0.00 MEMB ATOM 6414 H13Y POPA 22 -16.321 20.046 0.491 1.00 0.00 MEMB ATOM 6415 C314 POPA 22 -18.396 19.961 -0.111 1.00 1.01 MEMB ATOM 6416 H14X POPA 22 -18.686 20.951 0.204 1.00 0.00 MEMB ATOM 6417 H14Y POPA 22 -19.197 19.234 0.080 1.00 0.00 MEMB ATOM 6418 C315 POPA 22 -18.024 19.833 -1.597 1.00 1.92 MEMB ATOM 6419 H15X POPA 22 -17.663 18.829 -1.906 1.00 0.00 MEMB ATOM 6420 H15Y POPA 22 -17.169 20.513 -1.796 1.00 0.00 MEMB ATOM 6421 C316 POPA 22 -19.239 20.200 -2.506 1.00 3.28 MEMB ATOM 6422 H16X POPA 22 -19.011 19.979 -3.570 1.00 0.00 MEMB ATOM 6423 H16Y POPA 22 -19.546 21.266 -2.437 1.00 0.00 MEMB ATOM 6424 H16Z POPA 22 -20.104 19.539 -2.286 1.00 0.00 MEMB thank you very much best Albert On 04/15/2013 08:03 PM, Albert wrote: Hello Justin and bv08ay: thanks a lot for kind reply. I count each component by isolating them one by one: 1. protein generated by pdb2gmx command: 4739 atoms in all 2. ligand: 79 atoms 3. chelostrol: 74x42= 3108 atoms 4. popc: 116x96= 11368 atoms 5. solvent: 10079x3= 30237 atoms total: 49531 all the above results I double check the no. of coponent and total line (which represent the atom no.) with gedit, the total atoms is 49621. The toplogy give correct no. of each component, and the total no. of such component should be 49621 instead of what claimed by Gromacs " does not match topology (topol.top, 51295) " It is correct with the topology I defined at the end of topol.top file: [ molecules ] ; Compound#mo
Re: [gmx-users] why no. of atoms doesn't match?
Hello Justin and bv08ay: thanks a lot for kind reply. I count each component by isolating them one by one: 1. protein generated by pdb2gmx command: 4739 atoms in all 2. ligand: 79 atoms 3. chelostrol: 74x42= 3108 atoms 4. popc: 116x96= 11368 atoms 5. solvent: 10079x3= 30237 atoms total: 49531 all the above results I double check the no. of coponent and total line (which represent the atom no.) with gedit, the total atoms is 49621. The toplogy give correct no. of each component, and the total no. of such component should be 49621 instead of what claimed by Gromacs " does not match topology (topol.top, 51295) " It is correct with the topology I defined at the end of topol.top file: [ molecules ] ; Compound#mols Protein 1 LIG1 CHL142 POPC98 SOL10079 thank you very much best Albert On 04/15/2013 07:45 PM, Justin Lemkul wrote: Seriously though, the answer to this question is always the same. You're not counting something right. The solution is something only you can determine. Applying grep -c is your friend here. You're off by 1764 atoms, which may be useful information if any of your molecules are evenly divisible into 1764. Water is, but perhaps other molecules are, as well, depending on their representation. -Justin -- 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] why no. of atoms doesn't match?
Hello: I've build a protein/membrane system with CHARMM-GUI, and I am going to use it for Gromacs MD simulation with Slipids FF. First I extract the protein and generate toplogy file by command: pdb2gmx -f protein.pdb -o gmx.pdb -ignh -ter The protein was assigned with Amber FF including TIP3P for solvent after that, I add the following at the top of topol.top file: ; Include forcefield parameters #include "slipids.ff/forcefield.itp" #include "ligand.itp" #include "popc.itp" #include "chol.itp" and the following at the bottom of topol.top file: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 CHL1 42 POPC 98 SOL 10079 A the new protein coordinate gmx.pdb was replaced CHEARMM-GUI protein coordinate, all cheloest are put together, all popc were also put together. The order in the complex.pdb are: protein, ligand, cholestrol, popc and water. The system contains 1 protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water molecules. Then I am trying to minimize the system with command: grompp_mpi -f em.mdp -c complex.pdb -o em.tpr However, it always failed with messages: Program grompp_mpi, VERSION 4.6.1 Source code file: /home/albert/Desktop/gromacs-4.6.1/src/kernel/grompp.c, line: 563 Fatal error: number of coordinates in coordinate file (complex.pdb, 49531) does not match topology (topol.top, 51295) I don't understand why Gromacs claim such kind of errors, since to me, everything is all right for my pdb file and toplogy... thank you very much Albert -- 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] shall we add ions in FEP?
Hello: I found that in the free energy calculation tutorial, the ligand was placed in "pure" solvent which doesn't have any ions. I am just wondering, will it be better to add 0.15 M NaCl in the system especially when we would like to calculate protein/ligand binding energy through FEP? THX Albert -- 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] how to extract last frame?
Hello: I am trying to extract last frame of my MD simulations with command: trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb but it said: WARNING no output, last frame read at t=751.4 gcq#286: "Oh, There Goes Gravity" (Eminem) thank you very much best Albert -- 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] can we use GPU from another machine for calculation?
Hello: I've got two GPU workstation both of which have two GTX690 GPU. Now I am planning to run Gromacs GPU version and I am just wondering can we submit a single GPU jobs in one machine and evoke all GPU resources from both machine? thank you very much best Albert -- 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] fail to pull
IC. thanks a lot for explanations. Albert On 04/07/2013 06:08 PM, Justin Lemkul wrote: I'm assuming you're getting that line from my tutorial. You pass the .cpt file to grompp to preserve velocities from the previous equilibration phase. If you don't, what was the point of equilibrating? Coordinates, topology, and .mdp parameters are all that are strictly required to produce a .tpr file, but other files may be necessary to produce a sensible .tpr file based on previous steps. -Justin -- 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] fail to pull
hello Justine: thanks a lot for such kind comments. I may find the problem, the COM probably is not suitable to use whole protein since I found by g_dist that all the distance are between 0.9-1.0 nm throughout the whole pulling process. BTW, I notice that we are using command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr for pulling .tpr generating. May I ask whey shall we use option "-t npt.cpt" in this step? Usually we only need to specify .mdp, .gro and .top file for .tpr file thank you very much best Albert On 04/07/2013 05:31 PM, Justin Lemkul wrote: Let me clear one thing up first. 1 ns of pulling with a 0.001 nm/ps pull rate will not necessarily cause the ligand to be displaced by 1 nm. The particle pulling the virtual spring will be displaced by 1 nm, but the ligand will only move as a function of this applied force and the restoring forces (i.e. interactions between the ligand and protein). Choosing a more suitable reference group and running the simulation for longer will produce the desired result. -Justin -- 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] fail to pull
On 04/06/2013 08:52 PM, Justin Lemkul wrote: Hard to tell. Does your ligand have a suitable exit pathway exactly aligned along the x-axis? Have you tried increasing the pull rate? How long is the simulation? I don't even see nsteps in the above .mdp file. How about increasing the force constant? Is the vector connecting the COM of the entire protein and the COM of the ligand suitable for describing the exit pathway? -Justin Hello Justin: thanks a lot for kind rely. Yes, I adjust the conformation of whole protein/ligand so that it can exist from X-axies. I only show part of the .mdp file so some of then are not shown. ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 50; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 1000 nstxtcout = 1000 ; every 1 ps nstenergy = 1000 probably I should consider use part of the protein such as residues around binding pocket as COM for protein instead of whole protein? I applied for 1ns with rate pull_rate1= 0.001, so at then end of pulling, the distance for COMprotein and COM ligand should be 10A. Probably this is too short for whole protein as COM? thank you very much best Albert -- 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] fail to pull
Dear: I am trying to pull my ligand outside of the binding pocket with following configurations: title = Umbrella pulling simulation define = -DPOSRES ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Tcoupl = v-rescale tc_grps = Protein_LIG Water_and_ions tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 ref_p = 1.0 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres It is quite strange, the ligand is still in place and not outside the pocket at the end of simulations. I am just wondering where is the problem? thank you very much best Albert -- 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
