*file alfadrest.itp* [ distance_restraints ] ; i j ? label funct lo up1 up2 weight 8002 10641 1 0 1 0.4 0.5 0.6 1 8040 10616 1 0 1 0.4 0.5 0.6 1 8067 10582 1 0 1 0.4 0.5 0.6 1 8104 10554 1 0 1 0.4 0.5 0.6 1 8283 10698 1 0 1 0.4 0.5 0.6 1 8259 10723 1 0 1 0.4 0.5 0.6 1 8222 10764 1 0 1 0.4 0.5 0.6 1 8189 10794 1 0 1 0.4 0.5 0.6 1 *file topol.top*
; Include Distance restraint file #ifdef DISRES #include "alfadrest.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "gromos43a1.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos43a1.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 *file .mdp* ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run define = -DDISRES ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force < 1.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 500000 ; 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) ;Parametros distance restraint disre = simple ; simple (per-molecule) distance restraints disre_fc = 1000 ; Force constant for distance restraints *Questions* 1.When I am doing the minimization it comes out this message: /Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 349 steps, but did not reach the requested Fmax < 10. / What this implies, can i continue besides this message?Or it is better to do something about it? 2.Can you recomend considerable literature on vacuum simulation? -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001391.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
