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<DIV>Can increase the emtol from 1000 to 10000 KJ <SPAN style="FONT-SIZE: 10pt; COLOR: black; LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'">mol <SUP>- 1</SUP> nm<SUP>-1?</SUP></SPAN></DIV>
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<DIV><SPAN style="FONT-SIZE: 10pt; COLOR: black; LINE-HEIGHT: 115%; FONT-FAMILY: 'Arial','sans-serif'"><SUP><FONT size=3>subarna</FONT></SUP></SPAN></DIV>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Mark Abraham <Mark.Abraham@anu.edu.au><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <gmx-users@gromacs.org><BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Thu, 10 December, 2009 2:33:23 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] energy minimization<BR></FONT><BR>subarna thakur wrote:<BR>> I am doing the energy minimization of a protein using the following keywords in em.mdp file-<BR>> cpp = /usr/bin/cpp<BR>> define = -DFLEX_SPC<BR>> constraints = none<BR>> integrator = steep<BR>> nsteps = 3000<BR>> ;<BR>> ; Energy minimizing
stuff<BR>> ;<BR>> emtol = 1000<BR>> emstep = 0.01<BR>> <BR>> nstcomm = 1<BR>> ns_type = grid<BR>> rlist = 1<BR>> coulombtype = PME<BR>> rcoulomb = 1.0<BR>> rvdw = 1.0<BR>> Tcoupl = no<BR>> Pcoupl = no<BR>> gen_vel = no<BR>> <BR>> -----------------------------------------------------------------<BR>> I am getting the ouput as following---------<BR>> Steepest
Descents converged to machine precision in 67 steps,<BR>> but did not reach the requested Fmax < 1000.<BR>> Potential Energy = -4.0967048e+06<BR>> Maximum force = 3.7720719e+04 on atom 5530<BR>> Norm of force = 1.7014005e+02<BR>> -----------------------------<BR>> Can anybody suggest what changes I can make<BR><BR>Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong.<BR><BR>Mark<BR>-- gmx-users mailing list <A href="http://in.mg50.mail.yahoo.com/dc/mailto%3A%25e%25" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://lists..gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A>
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