[gmx-users] Typo in table 3.1 of the reference manual?
Dear all, There is an inconsistency in the truncated octahedron entry in table 3.1 of the reference manual (version 2018 and all previous ones I checked). The value indicated for the bc and ab angles is 71.53 degrees, but the vectors a, b and c indicated in the table give the value 70.53 degrees = acos(1/3). The indicated vectors correspond indeed to one of the possible sets of primitive vectors in the body-centered cubic lattice of which the truncated octahedron is the Wigner-Seitz primitive cell (namely the set with origin at a cube corner and pointing to three cube centers), so I belive that the typo is in the angles, not the vectors. Or am I missing something? Best, Antonio -- António M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Domain Decomposition
Hi, You have a bonded interaction at a distance of 10 nm. I assume that's not your intention. Perhaps you should give a configuration to grompp that has whole molecules. IIRC less ancient versions of GROMACS do a better job of this. Mark On Thu, Feb 15, 2018 at 5:39 PM Iman Ahmadabadi wrote: > Dear Gromacs Users, > > In one job, I always get in (any number of nodes) the domain decomposition > error as following and I don't know what should I do. I have to use the > -dds or -rdd setting for my problem? > > Sincerely > Iman > > Initializing Domain Decomposition on 56 nodes > Dynamic load balancing: auto > Will sort the charge groups at every domain (re)decomposition > Initial maximum inter charge-group distances: > two-body bonded interactions: 9.579 nm, LJ-14, atoms 1663 1728 > multi-body bonded interactions: 9.579 nm, Angle, atoms 1727 1728 > Minimum cell size due to bonded interactions: 10.537 nm > Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.700 nm > Estimated maximum distance required for P-LINCS: 0.700 nm > Guess for relative PME load: 0.87 > Using 0 separate PME nodes, as guessed by mdrun > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 > Optimizing the DD grid for 56 cells with a minimum initial size of 13.171 > nm > The maximum allowed number of cells is: X 0 Y 0 Z 0 > > --- > Program mdrun, VERSION 4.6 > Source code file: /share/apps/gromacs/gromacs-4.6/src/mdlib/domdec.c, line: > 6767 > > Fatal error: > There is no domain decomposition for 56 nodes that is compatible with the > given box and a minimum cell size of 13.1712 nm > Change the number of nodes or mdrun option -rdd or -dds > Look in the log file for details on the domain decomposition > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx insert-molecule issue- not getting the number atoms inserted wanted
Hi, There's not enough information to say. What makes you think your molecules will fit in the spaces you say are there? What radii did you suggest for the atoms in your molecules? Mark On Thu, Feb 15, 2018 at 6:54 PM Joydeep Munshi wrote: > Hello, > > I have a system of polymer(P3HT)-fullerene system. I am using initially > Insert-molecule command to insert N number of P3HT molecules followed by > PCBM molecules. Finally I am solvating the system using Solvate command. > > While I am trying to insert N=300 atoms it is successfully inserting all of > them. However, while I am inserting more than 350 molecules, it is failing > to do that. I tried to increase -try flag to 25000-3 so that it can > insert. But I am failing to do that. > > However my box does have empty volume after inserting, say 350 P3HT > molecules, when it is failing to insert more. Is there any way to get this > done efficiently to insert more atoms to the system? > > Is there any option to insert molecules using parallel processing. > > Thanks in advance. > > *Thanks and regards,* > *Joydeep Munshi,* > *Graduate Research Assistant,* > *Packard Lab 375,* > *Mechanical Engineering and Mechanics,* > *Lehigh University* > *Contact: (484)-821-6702* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] compiling 2018 with GPU doesn't work on my debian stretch
Szilárd wrote:> Option A) Get a gcc 5.x (e.g. compile from source) > Option B) Install CUDA 9.1 (and required driver) which is compatible > with gcc 6.3 > (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) didn't try A (there might be a good reason why stretch does not have gcc-5), but B appears work, at least for 2016 will try 2018 next. thank you! Michael -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx insert-molecule issue- not getting the number atoms inserted wanted
Hello, I have a system of polymer(P3HT)-fullerene system. I am using initially Insert-molecule command to insert N number of P3HT molecules followed by PCBM molecules. Finally I am solvating the system using Solvate command. While I am trying to insert N=300 atoms it is successfully inserting all of them. However, while I am inserting more than 350 molecules, it is failing to do that. I tried to increase -try flag to 25000-3 so that it can insert. But I am failing to do that. However my box does have empty volume after inserting, say 350 P3HT molecules, when it is failing to insert more. Is there any way to get this done efficiently to insert more atoms to the system? Is there any option to insert molecules using parallel processing. Thanks in advance. *Thanks and regards,* *Joydeep Munshi,* *Graduate Research Assistant,* *Packard Lab 375,* *Mechanical Engineering and Mechanics,* *Lehigh University* *Contact: (484)-821-6702* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU problem with running gromacs.2018
Yes, it is true, sorry, but I have problems with both. With version 2018 the error it's diferent. that's why i compiled an older version. Osmany -Original Message- From: Szilárd Páll Reply-to: gmx-us...@gromacs.org To: Discussion list for GROMACS users Subject: Re: [gmx-users] GPU problem with running gromacs.2018 Date: Thu, 15 Feb 2018 18:23:51 +0100 PS: Also, what you pasted in here states "2016.4", but your subject claims version 2018 -- Szilárd On Thu, Feb 15, 2018 at 6:23 PM, Szilárd Páll wrote: > Please provide a full log file output. > -- > Szilárd > > > On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz > wrote: > > Hi > > > > I am having problems running mdrun command compiled with GPU > > support(cuda 9.0). > > here is the output of the mdrun command > > > > > > Using 1 MPI thread > > Using 4 OpenMP threads > > > > 1 compatible GPU is present, with ID 0 > > 1 GPU auto-selected for this run. > > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > > > > WARNING: Just caught a previously occurred CUDA error (no kernel > > image > > is available for execution on the device), will try to continue. > > > > > > --- > > Program: gmx mdrun, version 2016.4 > > Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) > > > > Fatal error: > > cudaFuncSetCacheConfig failed: invalid device function > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ... > > > > > > Thanks. > > Osmany > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/Support/Maili > > ng_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Flip a bilayer
Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in vmd, is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use option System. What can i do to flip the bilayer? should i use lipid and water options in index? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU problem with running gromacs.2018
PS: Also, what you pasted in here states "2016.4", but your subject claims version 2018 -- Szilárd On Thu, Feb 15, 2018 at 6:23 PM, Szilárd Páll wrote: > Please provide a full log file output. > -- > Szilárd > > > On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz > wrote: >> Hi >> >> I am having problems running mdrun command compiled with GPU >> support(cuda 9.0). >> here is the output of the mdrun command >> >> >> Using 1 MPI thread >> Using 4 OpenMP threads >> >> 1 compatible GPU is present, with ID 0 >> 1 GPU auto-selected for this run. >> Mapping of GPU ID to the 1 PP rank in this node: 0 >> >> >> WARNING: Just caught a previously occurred CUDA error (no kernel image >> is available for execution on the device), will try to continue. >> >> >> --- >> Program: gmx mdrun, version 2016.4 >> Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) >> >> Fatal error: >> cudaFuncSetCacheConfig failed: invalid device function >> >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ... >> >> >> Thanks. >> Osmany >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU problem with running gromacs.2018
Please provide a full log file output. -- Szilárd On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz wrote: > Hi > > I am having problems running mdrun command compiled with GPU > support(cuda 9.0). > here is the output of the mdrun command > > > Using 1 MPI thread > Using 4 OpenMP threads > > 1 compatible GPU is present, with ID 0 > 1 GPU auto-selected for this run. > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > WARNING: Just caught a previously occurred CUDA error (no kernel image > is available for execution on the device), will try to continue. > > > --- > Program: gmx mdrun, version 2016.4 > Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) > > Fatal error: > cudaFuncSetCacheConfig failed: invalid device function > > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > ... > > > Thanks. > Osmany > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU problem with running gromacs.2018
Hi I am having problems running mdrun command compiled with GPU support(cuda 9.0). here is the output of the mdrun command Using 1 MPI thread Using 4 OpenMP threads 1 compatible GPU is present, with ID 0 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 WARNING: Just caught a previously occurred CUDA error (no kernel image is available for execution on the device), will try to continue. --- Program: gmx mdrun, version 2016.4 Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) Fatal error: cudaFuncSetCacheConfig failed: invalid device function For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ... Thanks. Osmany -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Domain Decomposition
Dear Gromacs Users, In one job, I always get in (any number of nodes) the domain decomposition error as following and I don't know what should I do. I have to use the -dds or -rdd setting for my problem? Sincerely Iman Initializing Domain Decomposition on 56 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 9.579 nm, LJ-14, atoms 1663 1728 multi-body bonded interactions: 9.579 nm, Angle, atoms 1727 1728 Minimum cell size due to bonded interactions: 10.537 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.700 nm Estimated maximum distance required for P-LINCS: 0.700 nm Guess for relative PME load: 0.87 Using 0 separate PME nodes, as guessed by mdrun Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 56 cells with a minimum initial size of 13.171 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.6 Source code file: /share/apps/gromacs/gromacs-4.6/src/mdlib/domdec.c, line: 6767 Fatal error: There is no domain decomposition for 56 nodes that is compatible with the given box and a minimum cell size of 13.1712 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] further compilation issues on stretch
as compilation of gmx-2018 idn't work for me i went back to 2016.4 after some google-ing i found that the following commands work, and gmx compiles without any complaints... > cmake .. -DGMX_GPU=on -DNVML_FOUND=1 > -DNVML_LIBRARY=/usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1 > -DNVML_INCLUDE_DIR=/usr/include -DCUDA_NVCC_FLAGS='-ccbin clang-3.8' > make -j 12 however, when i do mdrun see in my log file: [...]Build OS/arch: Linux 4.9.0-4-amd64 x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 6.3.0 C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 6.3.0 C++ compiler flags: -mavx -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;-D_FORCE_INLINES;-ccbin clang-3.8;-Xcompiler;,-mavx,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,; CUDA driver: 8.0 CUDA runtime: 0.0 NOTE: Error occurred during GPU detection: unknown error Can not use GPU acceleration, will fall back to CPU kernels. [...] i have a vanilla version of debian stretch with nvidia drivers and toolkit installed from theofficial debian packages. my graphic card is Geforce GTX 780 my gcc is 6.3 (no 5 in stretch) i wonder if i installed the nvidia driver/toolkit as provided directly from nvidia would that makethings work .. or rather worse ?? thanks for any suggestions!michael === Why be happy when you could be normal? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] using enegygrps
Hi Dr.Lemkul Thank you very much for your answer, it was very great help for me Thank you Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] compiling 2018 with GPU doesn't work on my debian stretch
Option A) Get a gcc 5.x (e.g. compile from source) Option B) Install CUDA 9.1 (and required driver) which is compatible with gcc 6.3 (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) -- Szilárd On Thu, Feb 15, 2018 at 2:34 PM, Michael Brunsteiner wrote: > > Hi, > I have problems compiling gromacs-2018 (January 10 release) on debian stretch > (vanilla) > my specs: Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) > x86_64 GNU/Linux > gcc-6.3.0,Cuda compilation tools, release 8.0, V8.0.44 > graphics: Geforce GTX 780. > I do: >> cmake .. -DGMX_GPU=on > > works w/o complaints, but when i do make i get: >> make -j 12 > [...]CMake Error at cmake/gmxManageGPU.cmake:289 (message): > NVCC/C compiler combination does not seem to be supported. > > in https://wiki.debian.org/NvidiaGraphicsDrivers#Debian_9_.22Stretch.22-1 it > says: > "CUDA 8 only supports gcc 5.3.1, which is not available for Stretch. > To compile you need to add -ccbin clang-3.8 to the nvcc command line. " > so i say:> cmake .. -DGMX_GPU=on -DCUDA_NVCC_FLAGS='-ccbin clang-3.8'[...] > -- Check for working NVCC/C compiler combination - broken > CMake Error at cmake/gmxManageGPU.cmake:289 (message): > NVCC/C compiler combination does not seem to be supported. CUDA frequently > does not support the latest versions of the host compiler, so you might > want to try an earlier C/C++ compiler version and make sure your CUDA > compiler and driver are as recent as possible. > debian stretch (the current stable debian release) does not have gcc-5 ... > is there any way around this issue?? > cheersMichael > > === Why be happy when you could be normal? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] compiling 2018 with GPU doesn't work on my debian stretch
Hi, I have problems compiling gromacs-2018 (January 10 release) on debian stretch (vanilla) my specs: Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) x86_64 GNU/Linux gcc-6.3.0,Cuda compilation tools, release 8.0, V8.0.44 graphics: Geforce GTX 780. I do: > cmake .. -DGMX_GPU=on works w/o complaints, but when i do make i get: > make -j 12 [...]CMake Error at cmake/gmxManageGPU.cmake:289 (message): NVCC/C compiler combination does not seem to be supported. in https://wiki.debian.org/NvidiaGraphicsDrivers#Debian_9_.22Stretch.22-1 it says: "CUDA 8 only supports gcc 5.3.1, which is not available for Stretch. To compile you need to add -ccbin clang-3.8 to the nvcc command line. " so i say:> cmake .. -DGMX_GPU=on -DCUDA_NVCC_FLAGS='-ccbin clang-3.8'[...] -- Check for working NVCC/C compiler combination - broken CMake Error at cmake/gmxManageGPU.cmake:289 (message): NVCC/C compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C/C++ compiler version and make sure your CUDA compiler and driver are as recent as possible. debian stretch (the current stable debian release) does not have gcc-5 ... is there any way around this issue?? cheersMichael === Why be happy when you could be normal? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Rupture force definition
On 2/15/18 4:13 AM, Rakesh Mishra wrote: Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull protocol. See, here for pulling this system, I have restricted 1st residue of chain-A, and pulling last ( 22th) residue of chain-B, which is at the same side end just below the 1st residue of chain-A. ( means, both reference and pull groups are at the same end side ). Note- I am pulling this 22th residue of chain-B in the downward (-z) direction with negative rate. ( here pull group is below from the reference group) I also followed your advise to pull with negative rate with high spring constant. But in this case also, system is not moving in the downwards (-z ) direction. Interesting- But the most interesting case is that for the same system just discussed above, when I am applying pulling code with + rate even with smaller spring constant, then system is moving in downward (-z) direction. While In my thinking, because I have given +rate, so it should move in the + z direction. So, could it be possible that there is one thing that can also matter , i.e. whether, pull group is below and reference group is above . Because in the same system, when I pull 22the residue of chain-A w.r.t reference residue 1 of chain-B (which is slightly below from the pull residue 22th of chain-A) with the same +rate and spring constant. In this case pull group moves in the + z direction (upward), which I expect ( note- here pull group is slightly above from the reference group) So, this contradiction with effect based on the end side pulling and posing of reference and pull groups is making it surprise and trouble. How is the RNA oriented? Is the z-axis coincident with the helical axis? If so, that's a poor choice for a reaction coordinate and you should choose a different axis, orthogonal to the helix. Or just pull in all dimensions so that it's the total COM distance between the base pair. Remember, the tutorial is a special case in which a one-dimension pull made sense due to the inherent geometry of the unidirectional growth model of amyloid fibrils. Do not assume that all system should be treated this way. The negative pull rate means "bring the two specified groups together" not necessarily "pull along -z" so be sure your orientation convention aligns with what you're trying to do. -Justin On Wed, Feb 14, 2018 at 7:53 PM, Justin Lemkul wrote: On 2/14/18 7:31 AM, Rakesh Mishra wrote: Dear Justin, Can you explain something regarding this issue. I couldn't get resolve one problem. Though now I am able to make restrict (immobile ) the needed residue and pulled another one. But the contradiction that i am facing is that, when I am pulling with -rate (in negative z direction, as I want to pull the residue in the negative Z direction of box ) given below. Still there we see that pulling group is not moving the -ve direction of z. Your settings are right, so either you need a larger force constant to induce the motion or you need to wait longer for the restoring forces in the system (whatever they are) to be overcome by the biasing potential. -Justin pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = chain-A-start pull_group2_name = chain-B-end pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= distance ; simple distance increase pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate= -0.01 ; 0.01 nm per ps = 10 per 1 ns pull_coord1_k= 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance 0 Best On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra wrote: Thank you very much Justin. Here it is working but having some problem. pull_group2_name = chain_B35 is moving in the + z direction & pull_group4_name= chain_B26 is moving oppositely in the -z direction While I have given pull in +z direction for both the above group. Note - pull_group1_name = chain_A8 and pull_group3_name = chain_A17 are immobile here as well as acting as reference. On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul wrote: On 2/1/18 7:59 AM, Rakesh Mishra wrote: Dear Justin Here I am applying pull for two groups with respect to two reference group as following. ; Pull code pull= yes pull_ngroups= 4 pull_ncoords= 1 pull_group1_name= chain_A8 (reference also immobile ) pull_group2_name= chain_B35 (pulling group) pull_group3_name= chain_A17(reference also immobile) pull_group4_name= chain_B26(pulling) pull_coord1_type= umbrella ; harmonic biasing force
Re: [gmx-users] using enegygrps
On 2/15/18 4:17 AM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul you said, the breaking molecule occured because of period boudary condition, isn't it a problem? because before your answer I thought I must select bigger box in order to the breaking won't occur. but now I understand the beaking isn't a problem. I have another question, what is difference between LJ-14 and LJ-SR, I think LJ-SR is short range interaction and LJ-14 is long range, am I right? No. LJ-14 are intramolecular pair interactions (1-4 interactions). I have a 128 DPPC, one drug molecule and 19110 water molecule in my box. when I select LJSR-SOL-SOL , then I will get vdw interaction between water molecules, but when I select LJSR:drug-drug, will I get vdw interaction between atoms of drug? because there is only one drug molecule in my box . Yes, if there are interactions that are within the short-range cutoff but not included in the 1-4 pair list. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] using enegygrps
On 2/14/18 11:16 PM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul Thank you very much for your answer and your time I 'm using Gromos 54a7 force field, How can I find my force field is parametrized in such a way that the nonbonded energy decomposition has some physical meaning? In your case, such a calculation would not correspond to any real quantity. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs
Hi Justin, That makes sense, I've found where the parameters are Thanks for your help James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 14 February 2018 22:31:07 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs On 2/14/18 5:28 PM, Easton J.W. wrote: > Hi Justin, > > Many thanks for the detailed reply. > > I just wanted to check that it doesn't matter that the A2C and A3C are not > present in the bonded and non-bonded itp files for the forcefield? Should > this not have given an error? The topology snippet you showed an [atomtypes] directive with those types defined, so they were in fact in the nonbonded parameter list by virtue of being added just above the first [moleculetype], as is permitted in GROMACS topologies. If there were missing parameters, grompp would have failed with a fatal error, so presumably you also included the necessary bonded parameters somewhere, too. -Justin > Kind regards, > > James > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: 14 February 2018 14:43:35 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Potential issue using acpype to convert amber > topology to gromacs > > > > On 2/14/18 9:42 AM, Justin Lemkul wrote: >> >> On 2/14/18 9:33 AM, Easton J.W. wrote: >>> Thanks Justin, >>> >>> >>> Will this effect the interactions (both bonded and non-bonded) that >>> these atoms have, as their atom types are not in the forcefield itp >>> files? >> Missing atom types would cause grompp to fail; you'd never get to the >> point where a simulation would be affected. >> >> You're introducing custom atom types in the topology itself, and >> that's always legal before any [moleculetype] appears. The LJ >> parameters come from the [atomtypes] directive. Masses and charges >> present in that directive aren't used. >> > Actually, to clarify: *if* masses are present in the [atoms] directive > of a [moleculetype], then the masses found in [atomtypes] are not used. > Strictly speaking, it is not necessary to have explicit masses in > [atoms], though nearly all topologies do. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] using enegygrps
Hi Dr.Lemkul you said, the breaking molecule occured because of period boudary condition, isn't it a problem? because before your answer I thought I must select bigger box in order to the breaking won't occur. but now I understand the beaking isn't a problem. I have another question, what is difference between LJ-14 and LJ-SR, I think LJ-SR is short range interaction and LJ-14 is long range, am I right? I have a 128 DPPC, one drug molecule and 19110 water molecule in my box. when I select LJSR-SOL-SOL , then I will get vdw interaction between water molecules, but when I select LJSR:drug-drug, will I get vdw interaction between atoms of drug? because there is only one drug molecule in my box . Thank you very much for your time and your answer Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Rupture force definition
Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull protocol. See, here for pulling this system, I have restricted 1st residue of chain-A, and pulling last ( 22th) residue of chain-B, which is at the same side end just below the 1st residue of chain-A. ( means, both reference and pull groups are at the same end side ). Note- I am pulling this 22th residue of chain-B in the downward (-z) direction with negative rate. ( here pull group is below from the reference group) I also followed your advise to pull with negative rate with high spring constant. But in this case also, system is not moving in the downwards (-z ) direction. Interesting- But the most interesting case is that for the same system just discussed above, when I am applying pulling code with + rate even with smaller spring constant, then system is moving in downward (-z) direction. While In my thinking, because I have given +rate, so it should move in the + z direction. So, could it be possible that there is one thing that can also matter , i.e. whether, pull group is below and reference group is above . Because in the same system, when I pull 22the residue of chain-A w.r.t reference residue 1 of chain-B (which is slightly below from the pull residue 22th of chain-A) with the same +rate and spring constant. In this case pull group moves in the + z direction (upward), which I expect ( note- here pull group is slightly above from the reference group) So, this contradiction with effect based on the end side pulling and posing of reference and pull groups is making it surprise and trouble. On Wed, Feb 14, 2018 at 7:53 PM, Justin Lemkul wrote: > > > On 2/14/18 7:31 AM, Rakesh Mishra wrote: > >> Dear Justin, >> >> Can you explain something regarding this issue. >> >> I couldn't get resolve one problem. Though now I am able to make >> restrict (immobile ) >> the needed residue and pulled another one. >> But the contradiction that i am facing is that, when I am pulling with >> -rate (in negative z direction, as I want to pull >> the residue in the negative Z direction of box ) given below. >> Still there we see that pulling group is not moving the -ve direction of >> z. >> > > Your settings are right, so either you need a larger force constant to > induce the motion or you need to wait longer for the restoring forces in > the system (whatever they are) to be overcome by the biasing potential. > > -Justin > > >> pull = yes >> pull_ngroups = 2 >> pull_ncoords = 1 >> pull_group1_name = chain-A-start >> pull_group2_name = chain-B-end >> pull_coord1_type= umbrella ; harmonic biasing force >> pull_coord1_geometry= distance ; simple distance increase >> pull_coord1_groups = 1 2 >> pull_coord1_dim = N N Y >> pull_coord1_rate= -0.01 ; 0.01 nm per ps = 10 per 1 >> ns >> pull_coord1_k= 1000 ; kJ mol^-1 nm^-2 >> pull_coord1_start = yes ; define initial COM distance >> > >> 0 >> >> >> Best >> >> >> >> On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra >> wrote: >> >> Thank you very much Justin. >>> >>> Here it is working but having some problem. >>> pull_group2_name = chain_B35 is moving in the + z direction & >>> pull_group4_name= chain_B26 is moving oppositely in the -z direction >>> While I have given pull in +z direction for both the above group. >>> >>> Note - pull_group1_name = chain_A8 and pull_group3_name = chain_A17 are >>> immobile here as well as acting as reference. >>> >>> >>> On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul wrote: >>> >>> On 2/1/18 7:59 AM, Rakesh Mishra wrote: Dear Justin > > Here I am applying pull for two groups with respect to two reference > group > as following. > ; Pull code > pull= yes > pull_ngroups= 4 > pull_ncoords= 1 > pull_group1_name= chain_A8 (reference also immobile ) > pull_group2_name= chain_B35 (pulling group) > pull_group3_name= chain_A17(reference also immobile) > pull_group4_name= chain_B26(pulling) > pull_coord1_type= umbrella ; harmonic biasing force > pull_coord1_geometry= distance ; simple distance increase > pull_coord1_groups = 1 2 > pull_coord1_dim = N N Y > pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per 1 > ns > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > pull_coord1_start = yes ; define initial COM distance > > 0 > > In above protocol I want to make two reference group as > 1-chain_A8 2- chain_A17 > and two
Re: [gmx-users] Flexible and posres
Dear Justin and Mark, The define = -DPOSRES -DFLEXIBLE is correct and thank you so much for your help. Respectfully, Iman On Wed, Feb 14, 2018 at 11:17 PM, Iman Ahmadabadi < imanahmadabad...@gmail.com> wrote: > Dear Justin, > > Because there is a movement on atoms that posres should act on them, and > this condition doesn't occur when the flexible option is not used. > > Sincerely, > Iman > > On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi < > imanahmadabad...@gmail.com> wrote: > >> Dear Mark, >> >> I forgot the D in -DPOSRES in the previous email. However I used the >> "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint >> was not applied on the atoms. Is there another way to solve the problem? >> >> Respectfully, >> Iman >> >> On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi < >> imanahmadabad...@gmail.com> wrote: >> >>> Dear Gromacs Users, >>> >>> If I wanna use some flexible bonds and also use position restraint on >>> some other atoms, how should I do this? the error arises because 2 define = >>> -DFLEXIBLE and -POSRES is not allowed in the .mdp files. >>> >>> Respectfully >>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
