[gmx-users] topology file from glycam/gaff to gromacs
Dear Gromacs user , i am a new user to gromacs and i am planning to run an MD for sugar system with nanoatoms in gromacs, i will use glycame force field for sugar and gaff force field for the other, I have the following question about the topology file: 1-i produced the top file that is compatible to gromacs and i want to ask this is the top of the topology file, i will use 1-4 scale which is 1 as my reach requirement, but I need to include the force field line which come after these line, ;[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ ; 1 2 no 1 1 1-since am using glycam and gaff where to get the ffglycam.itp as well as gaff.itp to include them in the top file. 2-i used amb2gmx.pl to produce the top file, should i do them as individual first them combine them, or i can use the files that have both my systems togather and then use amb2gmx.pl thank you for the help in advance rasha alqus x.top created by rdparm2gmx.pl Thu Mar 19 13:54:18 GMT 2015 ;[ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ; 1 2 no 1 1 [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon H1H1 0. 0. A 2.47135e-01 6.56888e-02 HoHo 0. 0. A 3.56359e-02 1.25520e-01 haha 0. 0. A 2.59964e-01 6.27600e-02 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OsOs 0. 0. A 3.1e-01 7.11280e-01 caca 0. 0. A 3.39967e-01 3.59824e-01 CgCg 0. 0. A 3.39967e-01 4.57730e-01 OhOh 0. 0. A 3.06647e-01 8.80314e-01 [ moleculetype ] ; Namenrexcl x 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 Ho 1ROHHO1 10.44500 1.00 2 Oh 1ROH O1 2 -0.63900 16.00 3 Cg 20GB C1 30.38400 12.00 4 H2 20GB H1 40.0 1.00 5 Os 20GB O5 5 -0.47100 16.00 6 Cg 20GB C5 60.22500 12.00 . . . . . . . . . . 28 ca 3GRAC3A 280.0 12.00 29 ca 3GRAC4A 290.0 12.00 30 ca 3GRAC5A 300.0 12.00 31 ca 3GRAC6A 310.0 12.00 32 ca 3GRAC7A 320.0 12.00 33 ca 3GRAC8A 330.0 12.00 34 ca 3GRAC9A 340.0 12.00 35 ca 3GRAC0B 350.0 12.00 36 ca 3GRAC1B 360.0 12.00 37 ca 3GRAC2B 370.0 12.00 38 ca 3GRAC3B 380.0 12.00 . -- 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] Reg g_energy tool
Thank you justin for your kind reply. As you told me in previous mail , the g_energy tool is enough to calculate interacton energy (such as Coulombic and Vandeewaal's interaction , LJ interaction ) between groups but How to choose two groups simulataneously in command prompt for example if i want to calculate LJ-(SR) interaction energy between CNT and peptide1 How to choose these two groups. already I set energygrps = CNT peptide1 petide2 in mdp file thanks in advance -- 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] Installation problem on CRAY XC40----Gromacs-5.0.4
Dear All, I am trying to install Gromacs-5.0.4 on cray XC40 by using following combinations: (cmake-3.2.1 is compiled by myself, OS is Suse Linux X86_64) Combination 1: INTEL 15.0/13.0 , MKL / FFTW and MPI (Cray-MPICH-7.0.5) set FLAGS=-dynamic -O3 -funroll-loops cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on -DGMX_OPENMP=on -DGMX_GPU=off -DCMAKE_INSTALL_PREFIX=/gromacs-5.0.4/intel-mkl-mpi -DGMX_FFT_LIBRARY=mkl -DGMX_DOUBLE=off -DGMX_BUILD_UNITTESTS=ON -DGMX_X11=off -DCMAKE_C_FLAGS=$FLAGS -DCMAKE_CXX_FLAGS=$FLAGS -DCMAKE_PREFIX_PATH=/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/lib:/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/include:/opt/cray/mpt/7.0.5/gni/bin It is showing the following error: -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES MPI_C_INCLUDE_PATH) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH) CMake Error at cmake/gmxManageMPI.cmake:150 (message): MPI support requested, but no MPI compiler found. Either set the C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or set the variables reported missing for MPI_C above. Call Stack (most recent call first): CMakeLists.txt:464 (include) -- Configuring incomplete, errors occurred! Combination 2: INTEL 15.0/13.0, MKL / FFTW and MPI (Cray-MPICH-7.0.5), CUDA(cudatoolkit/5.5.22) It is showing the following error: [ 0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o In file included from /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/cuda_runtime.h(59), from /home/proj/14/physatya/c40/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/ pmalloc_cuda.cu(0): /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/host_config.h(72): error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! ^ CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build1/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I have tried with GNU PrgEnv also, but unable to install. Kindly help. With best regards, Satyabrata Das -- 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] CUDA fails to allocate memory to mdrun
Hi! I'm running gromacs v5.0.4 on a 32-bit CentOS 6.5 OS with CUDA toolkit v4.0 and the latest nvidia linux driver (v340.24) for a Quadro K4200. My explicit solvent runs crash during pme grid optimization citing the following error - - There are: 75766 Atoms Initial temperature: 301.154 K Started mdrun on rank 0 Mon Mar 30 14:30:54 2015 Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 6.92142e+03 9.29820e+03 3.90420e+02 3.61267e+03 4.01187e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 2.14594e+05 -9.79483e+03 -1.47636e+06 6.97759e+03 2.17547e-01 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.20424e+06 1.89766e+05 -1.01448e+06 3.01035e+02 -2.11354e+02 Pressure (bar) Constr. rmsd -4.75277e+02 2.75540e-05 step 80: timed with pme grid 60 60 60, coulomb cutoff 1.000: 3398.8 M-cycles Step Time Lambda 100 0.2 0.0 Energies (kJ/mol) Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 7.24215e+03 9.27752e+03 4.13476e+02 3.61128e+03 4.00927e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 2.17175e+05 -9.83595e+03 -1.47626e+06 4.92524e+03 8.51347e+02 Potential Kinetic En. Total Energy Temperature Pres. DC (bar) -1.20251e+06 1.87791e+05 -1.01472e+06 2.97902e+02 -2.13130e+02 Pressure (bar) Constr. rmsd -2.43339e+02 2.65826e-05 step 160: timed with pme grid 52 52 52, coulomb cutoff 1.102: 3359.8 M-cycles --- Program mdrun, VERSION 5.0.4 Source code file: /nmr/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 2851616 bytes failed: out of memory For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The size of the failed allocation varies from error to error but it generally ranges from 2.5 to 5 mB. While it is likely that the newer toolkits(v5-7) have resolved this issue, I am unable to use them since they lack support for 32-bit OSs. I would be obliged if you could suggest a way to free up some page-linked memory (at least that's what google says the problem is but I'm still all at sea as far as the solution goes) for mdrun and/or provide a patch for pmalloc_cuda.cu. The problem looks to be limited to complex systems [(large proteins (150 residues) in explicit water (~25000 molecules) cubes] as I am able to run smaller ones (~100 residues) with ease in explicit solvent using the GPU for non-bonded calculations (mdrun -v -deffnm $prot_md -nb gpu). I have attached herewith the corresponding log file and mdp. Regards, Akshay Kumar Ganguly Graduate Student,Dr. Neel S. Bhavesh lab, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi - 67 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4
Hi, You may want to read the Cray docs before attempting to compile on the machine. You need to use the compiler wrappers (cc/CC) if you want to run on the compute nodes and I suggest that you just use gcc 4.8/4.9 which will be both compatible with nvcc and faster. Cheers, -- Szilárd On Mon, Mar 30, 2015 at 4:13 PM, Satyabrata Das satyabrata...@gmail.com wrote: Dear All, I am trying to install Gromacs-5.0.4 on cray XC40 by using following combinations: (cmake-3.2.1 is compiled by myself, OS is Suse Linux X86_64) Combination 1: INTEL 15.0/13.0 , MKL / FFTW and MPI (Cray-MPICH-7.0.5) set FLAGS=-dynamic -O3 -funroll-loops cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on -DGMX_OPENMP=on -DGMX_GPU=off -DCMAKE_INSTALL_PREFIX=/gromacs-5.0.4/intel-mkl-mpi -DGMX_FFT_LIBRARY=mkl -DGMX_DOUBLE=off -DGMX_BUILD_UNITTESTS=ON -DGMX_X11=off -DCMAKE_C_FLAGS=$FLAGS -DCMAKE_CXX_FLAGS=$FLAGS -DCMAKE_PREFIX_PATH=/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/lib:/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/include:/opt/cray/mpt/7.0.5/gni/bin It is showing the following error: -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Could NOT find MPI_C (missing: MPI_C_LIBRARIES MPI_C_INCLUDE_PATH) -- Could NOT find MPI_CXX (missing: MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH) CMake Error at cmake/gmxManageMPI.cmake:150 (message): MPI support requested, but no MPI compiler found. Either set the C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or set the variables reported missing for MPI_C above. Call Stack (most recent call first): CMakeLists.txt:464 (include) -- Configuring incomplete, errors occurred! Combination 2: INTEL 15.0/13.0, MKL / FFTW and MPI (Cray-MPICH-7.0.5), CUDA(cudatoolkit/5.5.22) It is showing the following error: [ 0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o In file included from /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/cuda_runtime.h(59), from /home/proj/14/physatya/c40/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/ pmalloc_cuda.cu(0): /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/host_config.h(72): error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported! ^ CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build1/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I have tried with GNU PrgEnv also, but unable to install. Kindly help. With best regards, Satyabrata Das -- 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] CUDA fails to allocate memory to mdrun
Hi, You can run with CPU-GPU load balancing disabled (-notunepme), that should avoid the error. You will likely not loose much performance as the performance difference between the first two grid settings in the tuning output seems to be marginal. Cheers, -- Szilárd On Mon, Mar 30, 2015 at 12:31 PM, Akshay Kumar Ganguly akshaygang...@yahoo.co.in wrote: Hi! I'm running gromacs v5.0.4 on a 32-bit CentOS 6.5 OS with CUDA toolkit v4.0 and the latest nvidia linux driver (v340.24) for a Quadro K4200. My explicit solvent runs crash during pme grid optimization citing the following error - - There are: 75766 Atoms Initial temperature: 301.154 K Started mdrun on rank 0 Mon Mar 30 14:30:54 2015 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 6.92142e+039.29820e+033.90420e+023.61267e+034.01187e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 2.14594e+05 -9.79483e+03 -1.47636e+066.97759e+032.17547e-01 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -1.20424e+061.89766e+05 -1.01448e+063.01035e+02 -2.11354e+02 Pressure (bar) Constr. rmsd -4.75277e+022.75540e-05 step 80: timed with pme grid 60 60 60, coulomb cutoff 1.000: 3398.8 M-cycles Step Time Lambda 1000.20.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 7.24215e+039.27752e+034.13476e+023.61128e+034.00927e+04 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 2.17175e+05 -9.83595e+03 -1.47626e+064.92524e+038.51347e+02 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) -1.20251e+061.87791e+05 -1.01472e+062.97902e+02 -2.13130e+02 Pressure (bar) Constr. rmsd -2.43339e+022.65826e-05 step 160: timed with pme grid 52 52 52, coulomb cutoff 1.102: 3359.8 M-cycles --- Program mdrun, VERSION 5.0.4 Source code file: /nmr/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 2851616 bytes failed: out of memory For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The size of the failed allocation varies from error to error but it generally ranges from 2.5 to 5 mB. While it is likely that the newer toolkits(v5-7) have resolved this issue, I am unable to use them since they lack support for 32-bit OSs. I would be obliged if you could suggest a way to free up some page-linked memory (at least that's what google says the problem is but I'm still all at sea as far as the solution goes) for mdrun and/or provide a patch for pmalloc_cuda.cu. The problem looks to be limited to complex systems [(large proteins (150 residues) in explicit water (~25000 molecules) cubes] as I am able to run smaller ones (~100 residues) with ease in explicit solvent using the GPU for non-bonded calculations (mdrun -v -deffnm $prot_md -nb gpu). I have attached herewith the corresponding log file and mdp. Regards, Akshay Kumar Ganguly Graduate Student,Dr. Neel S. Bhavesh lab, Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi - 67 -- 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] Reg g_energy tool
On 3/30/15 9:37 AM, vidhya sankar wrote: Thank you justin for your kind reply. As you told me in previous mail , the g_energy tool is enough to calculate interacton energy (such as Coulombic and Vandeewaal's interaction , LJ interaction ) between groups but How to choose two groups simulataneously in command prompt for example if i want to calculate LJ-(SR) interaction energy between CNT and peptide1 How to choose these two groups. Have you actually tried running g_energy yet? It should be readily apparent what everything is. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] fixed number of clusters from a MD simulation
Dear Gromacs users, I am trying to find a method to obtain a fixed number of clusters (using g_cluster) from a MD simulation. The search of clusters is very manual, depending a lot of the cutoff selected for the analysis. Is there any way to calculate a fixed number of clusters from a MD simulation, in such way that the program calculates the proper cutoff to provide the exact number asked by the user? Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Spain -- 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] Setting custom atoms in FF
On 3/29/15 7:53 PM, Alex wrote: Another question about x2top: in the previous discussion, the atom type was determined from its environment and the element type. What if I set up my PDB with atom labels (i think that's the third field from the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the force field contains CJ1 opls_9960 12.011 3C 0.142 C 0.142 C 0.142 CJ2 opls_1001 0.112.011 3C 0.142 C 0.142 C 0.149 Will then the right distinction be made? I'm asking before trying it, because it is quite tedious for me to do the labeling. The issue is way beyond carbons, I just discovered that a bunch of different atoms isn't set up correctly. The element field can be up to 16 characters long, per the code (overkill, but it indicates that there should be some flexibility). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Setting custom atoms in FF
I am not sure if your answer was a resounding yes. I am talking about the label on the left in PDB. Let us say I want to name my atoms TEST1 and TEST2 and set up my PDB as ATOM 1 TEST1 CNT A 1 xxx yyy zzz 1.00 0.00 ATOM 2 TEST2 CNT A 1 xxx yyy zzz 1.00 0.00 and then in atomname2type.a2t I put TEST1 opls_9960 12.011 3C 0.142 C 0.142 C 0.142 TEST2 opls_1001 0.112.011 3C 0.142 C 0.142 C 0.149 will the resulting topology contain the distinction despite the issue with bond lengths? If not, what would be the correct syntax to do that? I just want to define my atoms in a way that supplements (actually, precedes) what x2top does when the atoms are not specifically labeled. A tedious solution in my case, but definitely viable, if this works. Thank you, Alex JL On 3/29/15 7:53 PM, Alex wrote: Another question about x2top: in the previous discussion, the atom type was determined from its environment and the element type. What if I set up my PDB with atom labels (i think that's the third field from the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the force field contains CJ1 opls_9960 12.011 3C 0.142 C 0.142 C 0.142 CJ2 opls_1001 0.112.011 3C 0.142 C 0.142 C 0.149 Will then the right distinction be made? I'm asking before trying it, because it is quite tedious for me to do the labeling. The issue is way beyond carbons, I just discovered that a bunch of different atoms isn't set up correctly. JL The element field can be up to 16 characters long, per the code (overkill, but JL it indicates that there should be some flexibility). JL -Justin JL -- JL == JL Justin A. Lemkul, Ph.D. JL Ruth L. Kirschstein NRSA Postdoctoral Fellow JL Department of Pharmaceutical Sciences JL School of Pharmacy JL Health Sciences Facility II, Room 629 JL University of Maryland, Baltimore JL 20 Penn St. JL Baltimore, MD 21201 JL jalem...@outerbanks.umaryland.edu | (410) 706-7441 JL http://mackerell.umaryland.edu/~jalemkul JL == -- Best regards, Alexmailto:nedoma...@gmail.com -- 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] regarding installation of gromacs
regards, when i atempt to copy the run files of cmake in bin there comes an error.The erroe shows as follow: (nautilus:7575): Gtk-WARNING **: Failed to register client: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.gnome.SessionManager was not provided by any .service files Nautilus-Share-Message: Called net usershare info but it failed: 'net usershare' returned error 255: net usershare: cannot open usershare directory /var/lib/samba/usershares. Error No such file or directory Please ask your system administrator to enable user sharing. (nautilus:7575): GLib-CRITICAL **: Source ID 116 was not found when attempting to remove it (nautilus:7575): GLib-CRITICAL **: Source ID 117 was not found when attempting to remove it (nautilus:7575): GLib-CRITICAL **: Source ID 118 was not found when attempting to remove it sggswu@sggswu-ThinkCentre-M73:~$ Please help me with the solution of this error. -- 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] Installation problem on CRAY XC40----Gromacs-5.0.4
Thank you, I will read Cray docs again, presently trying to install with gcc 4.8 because 4.9 is showing incompatibility error with the available cudatoolkit. It seems CPU-only installation is successful. However both built in test case and regression-test failed with the following error: [Tue Mar 31 00:44:27 2015] [c1-0c0s1n1] Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(506): MPID_Init(192)...: channel initialization failed MPID_Init(569)...: PMI2 init failed: 1 Kindly help, With best regards, Satyabrata Das -- 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.
