Dear Gromacs Users, I am trying to run a Normal Mode Analysis with Gromacs v5.0.4 of a structure of 18081 atoms (without water) and I have a problem. I did a several minimization of my structure (1 SD, 1 CD and 4 L-BFGS), and everything went well. You can see below the relative informations for my last L-BFGS minimization:
---------- At the top of my .log file: Using 10 BFGS correction steps. F-max = 9.76934e-06 on atom 15076 F-Norm = 7.50769e-07 ---------- At the end of my .log file: Low-Memory BFGS Minimizer converged to Fmax < 1e-07 in 132449 steps Potential Energy = -9.52896691013964e+04 Maximum force = 9.82970751734797e-08 on atom 17063 Norm of force = 1.69009515334513e-08 then, when I run my NMA, I see this message in my .log file: Maximum force: 2.85412e+02 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. My command line is : grompp_mpi_d -f nma.mdp -c em_BFGS_4_NoWater.gro -t em_BFGS_4_NoWater.trr -e em_BFGS_4_NoWater.edr -p protein.top -o nma_NoWater.tpr My question is why I have such a large force ? Thank you in advance for your help. -- 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.
