Dear all, I am trying to conduct some simple ligand binding studies for a protein system solvated in water. After inputting the command:
mdrun -v -deffnm em -nt 1 I get the log shown below, nothing completes after this 0 step. Any help would be appreciated. Back Off! I just backed up em.log to ./#em.log.14# Getting Loaded... Reading file em.tpr, VERSION 4.5.4 (single precision) Loaded with Money Back Off! I just backed up em.trr to ./#em.trr.3# Back Off! I just backed up em.edr to ./#em.edr.3# Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Warning: 1-4 interaction between 1 and 8 at distance 4.764 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size mdrun -v -deffnm em -nt[1]+ Segmentation fault: 11 mdrun -v -deffnm em -nt 1 104-142:GLY lwollmuth$ tail -15 em.log Configuring nonbonded kernels... Configuring standard C nonbonded kernels... Testing x86_64 SSE2 support... present. Removing pbc first time ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- The mdp input file is as below: title = Minimization ; Title of run ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) -- Rashek Kazi GS 2 MSTP Candidate
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
