hello I am doing a md with martini force filed,I create a box, there is a double monolayer, then I solvate it, but when I did energy minimization, gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then
NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 562058480 Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'DPPC' Excluding 1 bonded neighbours molecule type 'W' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 72143 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 261042.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118 Estimate for the relative computational load of the PME mesh part: 0.91 NOTE 2 [file minim.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. gmx mdrun -v -deffnm em Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.36880e+22 Fmax= inf, atom= 2016 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. writing lowest energy coordinates. it just stopped with 14 steps, here is my mdp file,if you can solve this problem, I will appreciate that. ; minim.mdp - used as input into grompp to generate em.tpr ; 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 < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization 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 cutoff-scheme = Verlet ; Buffered neighbor searching 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 in all 3 dimensions jiao -- 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.