Hi, How about trying md with very small step size such as dt = 0.0001 ? Once I had similar problem like you and it is solved by performing additional energy minimization step with very small step size. I can't guarentee this method, but I think it might be OK.
On 8/13/07, Q733 <[EMAIL PROTECTED]> wrote: > > Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of > 32 lipids(16 up and 16 down) with two water layers(428 up and 428 down). > my em.mdp is like this: > > title = > cpp = /lib/cpp > include = > define = -DFLEXIBLE > constraints = none ;h-bonds > lincs_iter = 4 > > ; RUN CONTROL PARAMETERS = > integrator = l-bfgs > > tinit = 0 > dt = 0.2 ; ps > nsteps = 6000 > > nstxtcout = 100 ; pos to xtc file > > nstlist = 5 > ns_type = grid > rlist = 0.7 > coulombtype = PME > rcoulomb = 0.7 > vdw-type = Cut-off > rvdw = 0.7 > fourierspacing = 0.095 ; default to 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > > ; ENERGY MINIMIZATION OPTIONS = > emtol = 0.00001 ; default > to 100 > emstep = 0.5 ; default to 0.01 > nstcgsteep = 1000 > > The em is done using double-precision gromacs program,and the out put is > like this: > > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1e-05 > > writing lowest energy coordinates. > > Low-Memory BFGS Minimizer converged to machine precision in 7 steps, > but did not reach the requested Fmax < 1e-05. > Potential Energy = 1.25811048952284e+15 > Maximum force = 5.23956606456297e+17 on atom 483 > Norm of force = 6.77707038974525e+15 > > How can I prevent it from converging to machine precision? Is there any > method to change the standard of machine precision? > Any suggestion will be appreciated , thanks a lot. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- -------------------------------------------------- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many object.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED]
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