> > > Hi all, > I ran energy minimization (em) step, (protein-CNT in water) by these > conditions: > title = Minimization > integrator = steep > emtol = 1000.0 > emstep = 0.01 > nsteps = 150000 > energygrps = Protein CNT > nstlist = 1 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > rvdw = 1.0 > pbc = xyz > > > but when it recieves to 40000 step (nearly), it gives error: > > Step= 125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= > 10656 > Step= 129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= > 10656 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > Double precision normally gives you higher accuracy. > > writing lowest energy coordinates. > > Back Off! I just backed up em2.gro to ./#em2.gro.1# > > Steepest Descents converged to machine precision in 130 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.7943236e+07 > Maximum force = 8.3583656e+04 on atom 10656 > Norm of force = 2.1333945e+03 > > then I ran my system with emtol=10 , but the error repeated too. then I ran > it by double-precision , but was not successful too. > > 1- I changed fmax value only in .mdp file, is it correct? or I should change > any parameter in topology file? > 2- is the nsteps too much ?and problem is long time?what is its problem?
________________________________ You have a maximum force on the order of 10^4, which is an order of magnitude higher than what you initially requested. mdrun is telling you that the problem is focused on atom 10656. Open up your structure in your visualization software of choice and find that atom. You likely have some unresolved clashes there that are causing this problem. justin Dear Justin first, I get error on atom number XXXX. after change emtol to 10 , I get same error on atom number YYYY. what' your idea? how to solve it? I use this file for PR step , but I get this error: A charge group moved too far between two domain decomposition your system might be not equilibrated well enough my system without charge (total charge is zero) what' your idea? thanks -- 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
