Hi gmx-users I am somehow famliar with gromacs but only used it with coarse grained force fields (Martini) so far, not with all atom ones. I am now trying to run a simulation on a membrane protein system (protein embedded in a POPC bilayer solvated with water) using the gromos force field (Gromacs 4.0.2 ffG53a). Using gromacs tutorials I managed to create the required input files (.gro, .top and .itp). I at at the stage of running a energy minimization using position restraints on the protein and the peptide molecules. I can grompp the input files
grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx with the following input file: ------------------------------ ------------------------------------------------------------------------------------- define = -DPOSRES -DPOSRES_LIPID integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; 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 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ------------------------------------------------------------------------------------------------------------------- and the following topology file ------------------------------------------------------------------------------------------------------------------- ; Include forcefield parameters #include "ffG53a6_lipid.itp" ; Include chain topologies #include "protein.itp" ; Include Position restraint file #ifdef POSRES #include "posre_protein.itp" #endif ; Include POPC topology #include "popc.itp" #ifdef POSRES_LIPID #include "lipid_posre.itp" #endif ; Include water topology #include "spc.itp" ; Include generic topology for ions #include "ions.itp" [ system ] ; Name mscl protein with POPC bilayer [ molecules ] ; Compound #mols Protein 1 POPC 242 SOL 32145 CL- 91 NA+ 91 ------------------------------------------------------------------------------------------------------------------- When I run the simulation I get the following output after 16 steps of the minimisation ------------------------------------------------------------------------------------------------------------------- Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 100 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 16 steps, but did not reach the requested Fmax < 100. Potential Energy = 8.0175742e+17 Maximum force = inf on atom 4443 Norm of force = inf ------------------------------------------------------------------------------------------------------------------- It seems there is an infinite force on atom 4443 but I don't really understand what that means. The confout.gro structure looks ok ie the system has not "exploded". Should the protein not be restrained? How do I know my position restraints actually work? I tried increasing the force constant of the restraints or removing the restraints but still get the same output. I also tried adding -DFLEXIBLE since I am using the spc model, but still the same output. can anyone tell me what that message actually means and what is wrong with my system? thanks -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia
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