[gmx-users] Normal mode analysis
Dear all Gromacs user, I am trying to perform the Normal Mode Analysis protein-DNA complex in vacuum. As the complex is highly negative charge (-163)I performed the energy minimization of complex in water (to neutralize the complex). After I get the completely minimized complex, again I have done energy minimization of complex (in vacuum) for just one step to get the .trr input file for the Normal mode analysis. As I have to perform the normal mode analysis in vacuum I did that. But due to highly negative charge it got stuck in hessian matrix calculation. Even though it calculate the matrix I got negative eigenvalues after diagonalizing the matrix. I also tried with complete energy minimization in vacuum and proceed for normal mode calculation, but again stuck with the same problem i.e. high negative charge (-163) How can I neutralize the system?? or there is any way to do that or probably I am doing something unusual?? Any suggestions will be very welcomed. Thanking you in advance! - Rahul -- 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] DNA-protein complex distorted in vacuum simulation
Dear all Gromacs user, I minimized the energy of my DNA-protein complex with steep, l-bfgs integrator, and then ran the mdrun with integrator = md in vacuum. Upto energy minimization part it ran fine. When I submitted the minimized structure for mdrun (vacuum), protein and DNA part jiggles around, also DNA part is unwinding (breaking bond) and distort the complex. During processing mdp file (gmx grompp -f md.mdp)I got one Note as follows NOTE 1 [file topol.top, line 44]: System has non-zero total charge: -163.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. As the system is highly negatively charged it would have caused the structure to distort or it could be an artifact of visualization software?? I have used following parameters for MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 10 ; 1 * 10 = 100ps dt = 0.001 ; 1 fs ; Output control nstxout = 1000 ; save coordinates every 10.0 ps nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps constraint_algorithm = lincs ; holonomic constraints cutoff-scheme= Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics constraints = none For energy minimization I have used following parameters ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 1 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 10 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) constraints = none same parameters for L-BFGS with change in integrator Could I use solvent for simulation or anything need to change Any help would be much appreciated. Thanking you in advance. - Rahul -- 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] Normal mode analysis error
Dear all, I am trying to perform the Normal Mode Analysis protein in water. Here is the .mdp file I am using: integrator = nm; time step nsteps = 10 ; number of steps nstlist = 10; update pairlist ns_type = grid ; pairlist methodi coulombtype = PME nstxtcout = 1.0 cutoff-scheme = Verlet rcoulomb= 1.0 rvdw= 1.0 ewald_rtol = 1.0 rlist = 1.0 ; cut-off for ns constraints = none define = -DWHATEVER And I get the error message: Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported. Any suggestions will be very welcomed. Thanking you in advance! -- - Rahul -- 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] mdrun crash
Dear Gromacs user, I am running mdrun to minimize (energy minimization) my structure co-ordinate, but every time it stuck by displaying following error Back Off! I just backed up em.log to ./#em.log.8# Reading file em.tpr, VERSION 5.0.4 (single precision) Using 1 MPI thread Using 16 OpenMP threads 1 GPU detected: #0: NVIDIA Quadro K600, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run. Mapping of GPU to the 1 PP rank in this node: #0 Setting the maximum number of constraint warnings to -1 Back Off! I just backed up em.trr to ./#em.trr.8# Back Off! I just backed up em.edr to ./#em.edr.8# Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=5 WARNING: Listed nonbonded interaction between particles 51227 and 51230 at distance 8.421 which is larger than the table limit 2.000 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. step= 0, Dmax= 1.0e-02 nm, Epot= nan Fmax= 2.79093e+14, atom= 39526 Parameter file is following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1.4; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) constraints = none Please provide the solution to fix this error. Thanking you in advance. -- - Rahul -- 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] Build-Gromacs installation error
Hello Everyone, I am trying to install Gromacs on my computer. But after I run *cmake ..* command it display error -- Enabling native GPU acceleration -- 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! See also /home/rose/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeOutput.log. See also /home/rose/Software/Gromacs/gromacs-5.0.4/build-gromacs/CMakeFiles/CMakeError.log. -- - Rose -- 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] optimize cpu with gpu node for gromacs
Dear all Gromacs User, I am using one GPU node (NVIDIA Tesla C2050, 2.5 Gb ,6 core ) for simulation purpose on Intel(R) core I7 (3.0 *GHz, 16gb*) system. I did tested on this workstation with Gromacs 4.6. It seems from these that performance of GPU is imbalanced with CPU. It was showing shorter cut_off but I am using least of it. Using 1 MPI thread Using 8 OpenMP threads 1 GPU detected: #0: NVIDIA Tesla C2050, compute cap.: 2.0, ECC: yes, stat: compatible 1 GPU auto-selected for this run. Mapping of GPU to the 1 PP rank in this node: #0 starting mdrun 'Protein ' 50 steps, 1000.0 ps. Writing final coordinates. NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%) Time:26585.222 3827.438 694.6 1h03:47 (ns/day)(hour/ns) Performance: 22.5741.063 How to optimize this mdrun to get maximum use of GPU and accelerate the performance?. How many thread to be given? What to be optimized so that I can use for simulation purpose? Please let me know this is enough information. -- with regard Rahul - -- 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] MD for extracellular and transmembrane system
Dear all Gromacs user, I am knew to Gromacs for molecular dynamics. One off the hurdle I encountered is that can I use GROMACS for modelling protein with extracellular and transmembrane domain i.e., maintain water/lipid system in molecular dynamics simulation. Can I add the water system for extracellular domain and lipid system for transmembrane domain in GROMACS? if yes please provide necessary information. -- - Rahul Dhakne Research Scholar, NIPER (Mohali). in.linkedin.com/in/rahul777/ -- 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.
