@ Justin, Thank you, that worked like a charm! (Using increased vanderwal distance)
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Jan 9, 2013, at 8:42 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: > Everytime I remove the atom that is causing the INF force, it gives me new > atom that causes INF force. (The ones that come up are all water beads that > are causing the infinite force), does that mean when i did genbox it inserted > water incorrectly? (Because I viewed it in VMD< it's certainly not > overlapping with my solute. ) > > Xu Dong Huang > Chemical & Biochemical Engineering > Rutgers School of Engineering > xudo...@eden.rutgers.edu > > On Jan 9, 2013, at 8:12 PM, Xu Dong Huang <xudo...@eden.rutgers.edu> wrote: > >> Dear users, >> >> Now I fixed the initial structure error, and I solvated it in water (martini >> bead model), and i run typical EM, I get the following error: >> >> Steepest Descents: >> Tolerance (Fmax) = 1.00000e+01 >> Number of steps = 50000 >> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fmax= inf, atom= >> 14524 >> 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. >> >> writing lowest energy coordinates. >> >> Steepest Descents converged to machine precision in 15 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = 4.4832208e+19 >> Maximum force = inf on atom 14524 >> Norm of force = inf >> >> gcq#182: "That Was Cool" (Beavis and Butthead) >> >> -----My EM.mdp file contains the following: >> integrator = steep >> dt = 0.020 >> nsteps = 50000 ;Note: 100 steps is to much for a vacuum >> run (nsteps=10) >> >> nstlog = 1000 >> nstenergy = 500 >> nstxtcout = 500 >> >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> periodic_molecules = no >> rlist = 1.4 >> >> coulombtype = Shift >> rcoulomb_switch = 0.0 >> rcoulomb = 1.2 >> epsilon_r = 15 >> epsilon_rf = 1 >> vdw_type = Shift >> rvdw_switch = 0.9 >> rvdw = 1.2 >> >> My system size 73191 W, and 1 star (consisted of 101 atoms) >> I read somewhere that it's that atom 14524 is overlapping… I can't visually >> see anything complicated in my VMD since the system is pretty big >> >> Xu Dong Huang >> Chemical & Biochemical Engineering >> Rutgers School of Engineering >> xudo...@eden.rutgers.edu >> >> -- >> 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 > > -- > 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 -- 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
