Hi, <br><br>How about trying md with very small step size such as <br> dt = 0.0001 <br>?<br>Once I had similar problem like you and it is solved by performing additional energy minimization step with very small step size.
<br>I can't guarentee this method, but I think it might be OK. <br><br><div><span class="gmail_quote">On 8/13/07, <b class="gmail_sendername">Q733</b> <<a href="mailto:sansanqin00@mails.tsinghua.edu.cn">sansanqin00@mails.tsinghua.edu.cn
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello, gmx-users,I tried to energy minimize a lipidbilayer consisting of
<br>32 lipids(16 up and 16 down) with two water layers(428 up and 428 down).<br>my em.mdp is like this:<br><br>title =<br>cpp = /lib/cpp<br>include =<br>define = -DFLEXIBLE
<br>constraints = none ;h-bonds<br>lincs_iter = 4<br><br>; RUN CONTROL PARAMETERS =<br>integrator = l-bfgs<br><br>tinit = 0<br>dt = 0.2 ; ps
<br>nsteps = 6000<br><br>nstxtcout = 100 ; pos to xtc file<br><br>nstlist = 5<br>ns_type = grid<br>rlist =
0.7<br>coulombtype = PME<br>rcoulomb = 0.7<br>vdw-type = Cut-off<br>rvdw =
0.7<br>fourierspacing = 0.095 ; default to 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4
<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br><br>; ENERGY MINIMIZATION OPTIONS =<br>emtol = 0.00001 ; default to 100<br>emstep =
0.5 ; default to 0.01<br>nstcgsteep = 1000<br><br>The em is done using double-precision gromacs program,and the out put is<br>like this:<br><br>Stepsize too small, or no change in energy.
<br>Converged to machine precision,<br>but not to the requested precision Fmax < 1e-05<br><br>writing lowest energy coordinates.<br><br>Low-Memory BFGS Minimizer converged to machine precision in 7 steps,<br>but did not reach the requested Fmax < 1e-05.
<br>Potential Energy = 1.25811048952284e+15<br>Maximum force = 5.23956606456297e+17 on atom 483<br>Norm of force = 6.77707038974525e+15<br><br>How can I prevent it from converging to machine precision? Is there any
<br>method to change the standard of machine precision?<br>Any suggestion will be appreciated , thanks a lot.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search
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<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'
<br>-Paul Dirac <br>'But he created too many object.'<br>-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">
sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a>